Manny Malhotra

Emmanuel Noveen Malhotra (born May 18, 1980) is a Canadian former professional ice hockey centre who is currently an assistant coach for the Toronto Maple Leafs of the National Hockey League (NHL). He is a former assistant coach of the Vancouver Canucks. He last played with the Lake Erie Monsters in the American Hockey League (AHL) on a try-out basis. During his 18-year career, he played as a centre for the Montreal Canadiens, Carolina Hurricanes, Vancouver Canucks, San Jose Sharks, Columbus Blue Jackets, Dallas Stars and the New York Rangers. Malhotra was known as a two-way forward and for his faceoff proficiency, in which he won over 56% of faceoffs he took in the NHL.

Malhotra held the distinction of being the last active player to have been a teammate of Wayne Gretzky.

## Playing career

Malhotra was drafted in the first round as the seventh overall pick of the 1998 NHL Entry Draft by the New York Rangers. He joined the NHL after a two-year career in the Ontario Hockey League (OHL) with the Guelph Storm, where he served as captain in his final year. Winning a J. Ross Robertson Cup championship and subsequently appearing in the 1998 Memorial Cup with the Storm, Malhotra also earned a Bobby Smith Trophy, George Parsons Trophy and Memorial Cup All-Star honours as a junior.

He played with the Rangers from 1998 to 2002. During this time he was assigned on numerous occasions to the team's AHL affiliate, the Hartford Wolf Pack, with whom he won a Calder Cup championship in 2000. At the 2001–02 trade deadline, he was dealt to the Stars and spent parts of three seasons with the club. Beginning in 2003–04, Malhotra began to see increased offensive production, marked by his acquisition off waivers by the Blue Jackets. After four seasons in Columbus, he signed a one-year contract with the Sharks in September 2009. He recorded a career-high in goals with San Jose, before joining the Canucks on a three-year deal. In his first season with Vancouver, Malhotra suffered a major injury to his left eye, requiring several surgeries. Despite having lost a significant amount of his vision, he returned the same year to compete in the 2011 Stanley Cup Finals. He struggled to play with the injury until Canucks management placed him on the injured reserve for the remainder of the 2012–13 season in February 2013.

Internationally, Malhotra has represented Canada in under-18 competition, two World Junior Championships and one World Championship. Serving as team captain at the 2000 World Junior Championships, Malhotra led Canada to a bronze medal.

### Guelph Storm

Malhotra played in the 1994 Quebec International Pee-Wee Hockey Tournament with the Mississauga Reps minor ice hockey team. After his time in the Metro Toronto Hockey League (MTHL), Malhotra was selected in the first round (17th overall) of the 1996 OHL Priority Selection, Malhotra played two seasons in the Ontario Hockey League (OHL) with the Guelph Storm, beginning in 1996–97. He scored 16 goals and 44 points over 61 games in his rookie season. In the 1997 playoffs, he added 14 points in 18 games as Guelph lost in the semi-finals to the Ottawa 67's. The following season, he improved to 16 goals and 51 points over 57 games. He served as team captain while being assigned the primary role of shutting down opposing team's top forwards. Guelph advanced to the OHL Finals, where they defeated Ottawa in five games to capture the J. Ross Robertson Cup. Malhotra had 13 points in 12 games in the championship-winning playoff season. Earning a berth into the 1998 Memorial Cup, Guelph made it to the final, where they lost to the Portland Winter Hawks 4–3 in overtime. Malhotra ranked third in tournament scoring with a goal and seven points over five games. He was named to the Memorial Cup All-Star Team and was awarded the George Parsons Trophy as the tournament's most sportsmanlike player.

### New York Rangers

In the off-season, Malhotra was drafted by the New York Rangers in the first round, seventh overall, of the 1998 NHL Entry Draft. The Rangers scouted him as a strong, physical player with good hockey sense and character, comparing him to Adam Graves. He was surprised to have been selected by the Rangers, as they were one of the only teams to have not interviewed or met with him prior to the draft. He anticipated being drafted by the Calgary Flames at sixth overall, as the team's general manager, Al Coates, had previously drafted him into the OHL as general manager of the Storm.

With the 1998–99 approaching, Malhotra had not yet signed an NHL contract with the Rangers by October. League rules stipulated that if he did not sign by October 8, 1998, he would be required to return to junior for the entire campaign. The night before the deadline, Malhotra and the Rangers agreed to a three-year deal worth the rookie-maximum of \$975,000 with performance-based incentives that could have increased his salary to \$2 million. Making the immediate jump from junior to the NHL at age 18, he became the second player of Indian heritage to play in the NHL. Malhotra recorded 8 goals and 16 points over 73 games as a rookie.

During the season, the Rangers were interested in acquiring Vancouver Canucks forward Pavel Bure. It was reported that Canucks general manager Brian Burke had requested Malhotra to be involved in a trade that would have sent him along with Niklas Sundström, Dan Cloutier and the Rangers' first-round pick in the 1999 draft in exchange for Bure. However, Rangers general manager Neil Smith refused to include Malhotra and the deal never materialized.

The following season, Malhotra struggled to earn a regular spot on the Rangers' roster and was often a healthy scratch. Rangers head coach John Muckler publicly declared before the beginning of Malhotra's second NHL campaign that he would be nothing more than a career third-liner. Malhotra's potential was often at the centre of an ongoing dispute between Muckler and Smith.

Malhotra suffered an ankle injury in November that sidelined him for four games. Upon his recovery, his play was judged by team management to have suffered and he began to be benched. Meanwhile, the Canadian national junior team wanted the Rangers to loan him to them for the 2000 World Junior Championships. On December 12, 1999, general manager Neil Smith obliged and assigned Malhotra for the international tournament. He was then sent for a two-week conditioning assignment with the Rangers' American Hockey League (AHL) affiliate, the Hartford Wolf Pack. On March 14, 2000, he was sent back down to the OHL in order to retain his eligibility for later AHL assignment in the season. Malhotra had dressed for only four games in the two months between his return from the World Junior Championships in early-January and his junior reassignment. He was pointless in the 27 games total he played with the Rangers that season.

Returning to Guelph, he played in five regular season and six playoff games. Upon his junior club's first-round playoff elimination, he was reassigned to the Wolf Pack where he recorded 1 goal and 6 points over 12 games to finish the regular season. He then added 3 points in 23 post-season contests, helping the Wolf Pack to the franchise's first Calder Cup championship.

Malhotra returned to the Wolf Pack the following season after failing to make the Rangers' roster out of training camp. With New York deep at the centre position, his AHL assignment was predicated on him learning to play wing. He received numerous call-ups to New York and finished the 2000–01 campaign with 11 points over 28 games in the AHL and 12 points over 50 games in the NHL. The season also marked a management change as Glen Sather took over as general manager, marking the departure of Smith, who had drafted Malhotra and regarded him as untradeable during his tenure.

Fifty-six games into his 2001–02 season with the Rangers, Sather dealt Malhotra to the Dallas Stars at the trade deadline, along with winger Barrett Heisten, in exchange for forwards Martin Ručinský and Roman Lyashenko. Although he had established himself as an effective forechecker and defensive forward, Malhotra did not materialize into the offensive player the Rangers hoped he would be.

### Post-New York

Malhotra welcomed the trade to Dallas as an opportunity for more playing time, as he was sparsely used with the Rangers. However, he saw limited success with the Stars. Following his trade, he recorded one point, a goal, in 16 games to finish the 2001–02 season. He was re-signed by Dallas to a two-year contract on June 27, 2002. In 2002–03, he recorded 10 points over 59 games. He appeared in his first Stanley Cup playoffs as the Stars qualified for the 2003 post-season as the top seed in the Western Conference. They were eliminated in the second round by the Mighty Ducks of Anaheim.

After going pointless in nine games early the following season, the Stars waived Malhotra on November 19, 2003. Two days later, he was picked up by the Columbus Blue Jackets. Malhotra improved with the Blue Jackets, notching 12 goals and 25 points over 56 games following the trade. He missed the final six games of the regular season with a bruised ankle. His ice time rose from an average of nine minutes a game with Dallas the previous season to 14 minutes in Columbus.

Due to the NHL lockout, Malhotra spent the 2004–05 season overseas in Europe. He initially signed with HDD Olimpija Ljubljana of Slovenia on October 8, 2004, and recorded 27 points over 26 games (including both Slovenian league and inter-league play). On December 12, he signed with HV71 of the Swedish Elite League. He notched seven points in 20 games with the club.

Returning to Columbus as NHL resumed play the following season, Malhotra spent 2005–06 centering Columbus' third line. Despite missing 24 games due to injury with back spasms in November and a shoulder injury in January, he improved his points total for the second-straight NHL season with 10 goals and 21 assists. The Blue Jackets re-signed him in the off-season to a three-year contract on June 20, 2006. In the first year of his new contract, he tallied nine goals and 25 points over a full 82-game season.

Malhotra missed 11 games with a recurring knee injury in December 2007. Late in the 2007–08 season, on March 17, 2008, he recorded a career-high three points in one game (two goals and an assist) in a 4–3 win against the Detroit Red Wings. He finished the campaign with 11 goals and 29 points. Early in the 2008–09 season, Malhotra missed five games with a lower-body injury. He recorded a career-high 24 assists and 35 points over 77 games during the campaign. As Columbus was plagued with numerous injuries over the course of the season, Malhotra was used on various lines while also in a shutdown role, playing against top opposing forwards.

His contract was not renewed by the Blue Jackets in the 2009 off-season and he became an unrestricted free agent. After failing to sign with an NHL team, Malhotra accepted an invitation to the San Jose Sharks' training camp on September 17, 2009. Five days later, he signed a one-year, \$700,000 deal with the team. He went on to record a career-high 14 goals and +17 rating, along with 19 assists for 33 points, in his only season with the Sharks. He centred the team's third line and earned time playing wing on the powerplay. However, the Sharks did not re-sign him and he became an unrestricted free agent for the second consecutive summer on July 1, 2010. Looking back on his time in San Jose, Malhotra called it the "most enjoyable season [he's] had as a pro", being able to play for a winning team and have a long playoff run for the first time in his NHL career.

### Vancouver Canucks

On his first day of free agency on July 1, 2010, Malhotra signed a three-year, \$7.5 million deal with the Vancouver Canucks that included a no-trade clause. Malhotra was named an alternate captain during away games for the Canucks before the season began. He scored his first goal as a Canuck on October 22, during a 5–1 win against the Minnesota Wild. Malhotra settled into the Canucks' lineup as the team's third-line centre, often playing with wingers Raffi Torres and Jannik Hansen, while playing significant time on the penalty kill and matching up against opposing team's best forwards. His success as a defensive specialist earned him early consideration for the Frank J. Selke Trophy as the league's best two-way forward. In an article on the NHL's website, he was chosen as the front-runner for the award at the mid-way point of the campaign. He was also credited with allowing the team to use Ryan Kesler in a more offensive role (Kesler was the team's previous shutdown centre); as a result, the second-line centre recorded career-highs in goals and points.

Near the end of the season, Malhotra was struck in the eye by a puck during a game against the Colorado Avalanche on March 16, 2011. He immediately left the ice and underwent eye surgery the following day. It was announced on March 21, 2011, that Malhotra would not be returning to the lineup for the rest of the regular season and the playoffs, without further comment on Malhotra's condition. Eight days later, he underwent a second successful surgery on his eye. Limited to 72 games, Malhotra recorded his third consecutive 30-point season with 11 goals and 19 assists while playing on the Canucks' third line alongside Raffi Torres and Jannik Hansen. His 61.7% faceoff percentage ranked second in the league behind David Steckel. The campaign also included the 100th goal of his NHL career, scored in a 3–0 win against the Anaheim Ducks on March 6, 2011.

On a team-basis, Malhotra's first season with the Canucks saw them earn the Presidents' Trophy for having the best regular season record in the league. In the midst of his recovery, Malhotra made an appearance during the team's pre-game ceremony at Rogers Arena, co-accepting the trophy with captain Henrik Sedin. Despite original statements from the team that he would not return for the playoffs, Malhotra began working his way up from light practices with the team in May 2011. By the end of the month, he was cleared by doctors to play in the Stanley Cup Finals. Though he remained out of the lineup for Game 1, he returned for the following contest and played the rest of the series as the team's fourth-line centre (late-season acquisition Maxim Lapierre filled in for Malhotra on the third line). Playing against the Boston Bruins, the Final went to a seventh game, which the Canucks lost. Malhotra's regular season performance earned him six first-place votes out of 125 for the Selke Trophy. He ranked fifth in balloting, as teammate Ryan Kesler won the distinction at the year-end Awards Ceremony.

Having lost a significant amount of his vision in his left eye, Malhotra struggled in his first full season since the injury in 2011–12. He was supplanted as the Canucks' third-line centre by rookie Cody Hodgson and later Samuel Påhlsson. Canucks head coach Alain Vigneault assessed Malhotra during the season as "not the same physical player he was before", adding, "He's still contributing but not maybe to the degree that he was before he got injured." Playing left wing on the fourth line, he remained an integral part of the team by playing on the penalty kill and taking important defensive zone faceoffs. Near the end of the campaign, Malhotra was chosen as the Canucks' nominee for the Bill Masterton Trophy, an annual NHL award for perseverance, sportsmanship and dedication to hockey. With a diminished offensive role, Malhotra finished his second season in Vancouver with 7 goals and 18 points over 78 games, as well as a –10 plus-minus rating. However, he remained among the league's elite in terms of faceoffs, ranking fourth with a 58.5% winning percentage.

Continuing to struggle with his eye injury, Malhotra was put on the injured reserve a month into the 2012–13 season. Fearing for his long-term health, Canucks general manager Mike Gillis took him out of the lineup for the season, a decision that he described as the "hardest thing [he has] done in [his] job". Malhotra had appeared in nine games without recording a point.

### Carolina Hurricanes

At the end of the 2013 NHL season, Malhotra became an unrestricted free agent. After being unsigned by an NHL team at the start of the 2013–14 season and looking to continue his playing career Malhotra signed a 25-game professional try out (PTO) contract with the AHL's Charlotte Checkers. The Carolina Hurricanes signed Malhotra to a one-year two way contract on October 31 and he made his Carolina debut against the New York Rangers on November 2. On November 6, he scored his first NHL goal in 19 months, scoring a game winner in overtime against the Philadelphia Flyers. As a measure of the amount of respect he has earned in the locker room in just a few weeks, Manny was selected to be an interim assistant captain while Tim Gleason was out with an injury. After Gleason was traded to the Toronto Maple Leafs, Malhotra was officially named an alternate captain for the remainder of the season.

### Montreal Canadiens

On July 1, 2014, Malhotra signed as a free agent to a one-year deal with the Montreal Canadiens. In the 2014–15 season, Malhotra was primarily used as the Canadiens fourth-line centre and face-off specialist. On February 28, 2015, he scored his first and only goal with Montreal in his 53rd appearance in a 4–0 victory over the Toronto Maple Leafs. Malhotra completed the season scoring only 4 points in 58 games.

On May 15, 2015, it was announced by Canadiens general manager Marc Bergevin that Malhotra would not return to the Canadiens for the next season. In July 2015, Malhotra officially became a free agent and proceeded to go un-signed over the summer. Two months into the 2015–16 season, Malhotra returned within the Columbus Blue Jackets organization by signing a professional try-out contract with American Hockey League affiliate, the Lake Erie Monsters on December 3, 2015.

## Coaching career

On September 7, 2016, the Vancouver Canucks announced that Malhotra would join the team as a development coach. This was announced shortly following his retirement.

On June 7, 2017, the Canucks announced that Malhotra was hired as assistant coach.

On September 17, 2020 Malhotra was hired as an assistant coach for the Toronto Maple Leafs.

## International career

In the summer of 1997, Malhotra captained Canada's under-18 team to a championship at the 3 Nations Cup in the Czech Republic. Canada finished as tournament champions, going undefeated over six games against the Czech Republic and Slovakia in the three-country competition.

The following year, Malhotra was named to the Canadian national under-20 team for the 1998 World Junior Championships, held in Finland. He was the second-youngest player on the team, behind Vincent Lecavalier. Malhotra was pointless in seven games as Canada was defeated in the quarter-finals by Russia, 2–1. The following year, he was not available for the tournament as he was playing in the NHL with the Rangers. However, in 2000, he was loaned to Team Canada by the Rangers' organization, as he was still eligible as a junior. Serving as team captain, he notched two assists over seven games in the tournament, held in Sweden. Canada earned the bronze medal, defeating the United States 4–3 in a shootout.

Malhotra debuted with Canada's men's team at the 2002 World Championships in Sweden. He recorded no points in seven games as Canada was eliminated in the quarter-finals by Slovakia.

## Personal life

Malhotra was born and raised in Mississauga, Ontario. His Punjabi Indian father, Shadi, was born in India and worked as a research chemist for Xerox at the Xerox Research Centre of Canada. His mother, Lise, is a French-Canadian and was a stay-at-home mom. Due to his mother's French background, he spoke both French and English at home. Malhotra has three siblings, two brothers and a sister.

Malhotra started playing organized hockey at age seven. He attended John Fraser Secondary School in Mississauga, before graduating from Our Lady of Lourdes in Guelph, Ontario. Malhotra moved to Guelph to begin his OHL career with the Guelph Storm, during which time he was awarded the Bobby Smith Trophy as the OHL's scholastic player of the year in 1998. He has referred to it as the award he is most proud of in his hockey career. In 2009, he received the National Leadership Award in a ceremony at his former high school in Guelph.

In his initial years with the Rangers, the organization arranged for him to live with former player Doug Sulliman and his family. In September 2007, Malhotra married Joann Nash, sister of National Basketball Association (NBA) star Steve Nash and former Vancouver Whitecaps FC midfielder Martin Nash and a soccer star herself, as captain of the University of Victoria women's soccer team. Malhotra and Joann have three sons.

## Career statistics

### Regular season and playoffs

### International

## Awards

## See also

- List of Indian NHL players

Canadian ice hockey player (born 1980)

Canadian expatriate ice hockey players in Slovenia

Canadian expatriate ice hockey players in Sweden

Canadian expatriate ice hockey players in the United States

National Hockey League first-round draft picks


Curley Byrd

Harry Clifton "Curley" Byrd (February 12, 1889 – October 2, 1970) was an American university administrator, educator, athlete, coach, and politician. Byrd began a long association with the University of Maryland as an undergraduate in 1905, and eventually rose to the position of university president from 1936 to 1954.

In the interim, he had also served as the university's athletic director and head coach for the football and baseball teams. Byrd amassed a 119–82–15 record in football from 1911 to 1934 and 88–73–4 record in baseball from 1913 to 1923. In graduate school at Georgetown University, he became one of football's early users of the newly legalized forward pass, and he had a brief baseball career including one season as pitcher for the San Francisco Seals.

Byrd resigned as university president in order to enter politics in 1954. He ran an unsuccessful campaign as the Democratic candidate for Maryland governor against Theodore McKeldin. Byrd later received appointments to state offices with responsibilities in the Potomac River and Chesapeake Bay. In the 1960s, he made unsuccessful bids for seats in each chamber of the United States Congress. Byrd was a proponent of a "separate but equal" status of racial segregation in his roles as both university administrator and political candidate.

In 2015, the Student Government Association agreed to a resolution in support of changing the name of Byrd Stadium because they noted that Byrd was "a racist and a segregationist" who "barred blacks from participating in sports and enrolling into the University until 1951". On September 28, 2015, University of Maryland President Wallace Loh appointed a task force to develop viewpoints and options. The University President then made a recommendation to the University System of Maryland Board of Regents — the governing body of Maryland state universities — to change the name to "Maryland Stadium". The ultimate decision on any name change rests with the Board of Regents. On December 11, 2015, the Board of Regents voted 12–5 to remove the "Byrd" from the stadium's name, renaming it Maryland Stadium for the time being.

## Early life

Harry Clifton Byrd was born on February 12, 1889, in Crisfield, Maryland. He was one of six children of oysterman and county commissioner William Franklin Byrd and his wife Sallie May Byrd. In his youth, Byrd worked in the Chesapeake Bay fishing industry, where he saved most of his money to finance his college education. He attended Crisfield High School, where he excelled on the baseball diamond, and was also known as his hometown's first recreational jogger.

A later source described how he appeared in 1905

> He was tall, and as the saying goes, built like a whip. He had a startlingly handsome face, with big, flashing eyes, a splotch of florid red on each cheek, and a mane of black curly hair ... He looked like Rupert of Hentzau, and had all of that worthy's cold, sinister resolution about everything that he did.

## College career

In 1905, Byrd graduated from Crisfield High School and enrolled at the Maryland Agricultural College, which is now known as the University of Maryland. Byrd was a star college athlete and participated in varsity football, baseball, and track. He served as the football team captain in 1907, as the pitcher on the baseball team, and set a school record 10.0-second 100-yard dash in track. Before leaving Crisfield, Byrd's father warned him not to "try to play that thing called football." He ignored the advice and reported for football practice where head coach Fred K. Nielsen told the undersized Byrd to "play with the kids" and that "football's a man's game." He was allowed, however, to fill in as an end on the scout team due to a shortage of players. After sitting out the first three games, Nielsen sent Byrd in as a substitute against Navy, and his play was impressive enough to earn a position on the first team. After the elder Byrd read of his son's newfound stardom in the newspaper, he wrote, "Since you're going to play football, I'm glad to see you're doing it well." During the summers and on weekends, Byrd supplemented his income by continuing work as a fisherman. He graduated second in his class with a Bachelor of Science degree in civil engineering in 1908.

After graduation from Maryland, Byrd spent the next three years doing graduate work in law and journalism at George Washington University, Georgetown University, and Western Maryland College (now known as McDaniel College). In a time before eligibility limitations, he played football at George Washington and Georgetown and ran track at Western Maryland. At Georgetown in 1909, he was called the first quarterback in the East to master the forward pass, several years before Gus Dorais of Notre Dame did so in 1913. According to The Georgetown Hoyas: A Story of A Rambunctious Football Team, Dorais's "end-over-end 'discus' throw was an exact copy" of Byrd's passing technique, and the Irish "got the headlines because they had a press agent and Georgetown didn't."

Byrd also played for Maryland-based semi-professional baseball teams while pursuing his graduate studies. In 1910, the Chicago White Sox signed Byrd, but he was soon traded to the San Francisco Seals, a semi-professional Pacific Coast League baseball team for whom he pitched in 1912. He returned to Maryland later that year, and in 1913, married Katherine Dunlop Turnbull. Before they divorced twenty years later, the couple had three sons and a daughter: Harry, Sterling, William, and Evelyn.

## Coaching career

In 1911, injuries claimed enough Maryland Agricultural football players that the team could no longer field a practice squad to scrimmage against. The college turned to Byrd, who was serving as coach at Western High School in Georgetown, and he was willing to help his alma mater with scrimmages. Byrd later replaced head coach Charley Donnelly, who resigned mid-season after accumulating a 2–4–2 record. Byrd led the Aggies to wins in both of their final games of the season, against Western Maryland, 6–0, and Gallaudet, 6–2.

In 1913, the Maryland Agricultural College hired Byrd as an instructor in English and history, and he was named the head coach of the track and baseball teams, the latter of which he coached through 1923. According to author David Ungrady in Tales from the Maryland Terrapins, the university initially offered Byrd \$300 to coach football, but he demanded \$1,200. The two parties came to agree upon that salary for all of his coaching and teaching duties which spanned nine months of the year. Byrd also worked as a sportswriter for The Washington Star, a job he held until 1932.

As football coach, he developed a unique offensive scheme called the "Byrd system", which combined elements of the single-wing and double-wing formations. One of Byrd's track and football players, Geary Eppley, said, "He never yelled in practice or at a game ... He pointed out mistakes and explained what you did wrong. He took a calm approach. The strongest thing he'd say was 'for cripes sake.'"

In 1915, his duties were expanded to include those of athletic director. That same year, he requested funds for the construction of the campus's first dedicated football stadium, which was named in his honor. During his tenure as head football coach from 1911 to 1934, he compiled a 119–82–15 record.

## Administrative career

Byrd was appointed to the post of assistant university president in 1918. He became a proponent of unification of the Maryland Agricultural College and the Baltimore professional schools into a single public University of Maryland, and he was instrumental in what became the Consolidation Act of 1920. Byrd named the student newspaper The Diamondback in 1921, and in 1933, he was the lead advocate for the adoption of the diamondback terrapin as the university's official nickname and mascot.

In 1932, Byrd was promoted to vice president of the university. In July 1935, he was named the acting president of the university, and was officially appointed to the presidency in February 1936. During his tenure, the budget, facilities, faculty, and enrollment increased significantly. The school budget was increased and the campus expanded largely due to Byrd's deft political maneuvering in Annapolis and Washington. The school also saw a large growth in enrollment, due in part to returning veterans making use of the G.I. Bill after World War II. From 1945 to 1948, the university budget increased from \$4.8 million to \$9.8 million. Between 1935 and 1954, student enrollment grew from 3,400 to 16,000. Over that same time period, the value of the campus rose from \$5 million to \$65 million. Byrd, however stood fast on faculty salaries. He reportedly said, "Ph.D.s are a dime a dozen." For years, Byrd refused to release the university's financial records to state legislators, and how exactly he secured funding for many of his projects was largely a mystery. According to booster Jack Heise, Byrd financed a new basketball arena through the out-of-state tuition, paid by the federal government, for Maryland high school graduates who attended the university on the G.I. Bill. The General Accounting Office calculated that the extra fees totaled more than \$2 million, but determined that they were within the bounds of legality.

Byrd was a staunch supporter of a "separate but equal" state university system. The Princess Anne campus provided agricultural education and Morgan State College provided liberal arts education for the state's black students, while the University of Maryland remained open only to white students. In 1951, Governor Theodore McKeldin criticized the University of Maryland as an example of wasteful state spending, and was especially critical of expansions to the Princess Anne campus, which was geographically disconnected from the state's black population and not attracting many students to study agriculture. Contractors had begun projects at the college before approval from the public works board, which was described as a usual practice under Byrd. Byrd acceded to McKeldin and secured approval from the board for both the Princess Anne expansions as well as a sizable increase to the university budget.

In 1945, Byrd hired 32-year-old Paul "Bear" Bryant to his first head coaching post. Bryant led the Terrapins to a 6–2–1 record, but the two personalities clashed. The tensions came to a head when Byrd reinstated a player Bryant had suspended for violating team rules. Bryant resigned as head coach an hour later, which caused an uproar among students until he interceded to restore order.

Two years later, Byrd hired Jim Tatum as football coach. The year prior at Oklahoma, Tatum fielded a winning team, but the athletic department ran up a huge deficit and some players were paid in violation of conference rules, which resulted in university president George Cross firing athletic director Jap Haskell. The media blamed Tatum for his termination. Tatum told Cross to refute Tatum's role in the matter, and threatened to reveal the Oklahoma team had been paid \$6,000 after the 1947 Gator Bowl. Cross asked Byrd to persuade Tatum not to go public, and according to author Gary King in An Autumn Remembered, Byrd replied, "Persuade, hell! I'll tell him to keep his damn mouth shut!" Tatum remained as coach at Maryland from 1947 to 1955, and amassed a 73–15–4 record.

In 1948, the National Collegiate Athletic Association passed a set of regulations called the Purity Code, later renamed the Sanity Code, which permitted student-athletes free tuition and meals, but required that part-time jobs be legitimate and their pay commensurate with the work. Schools found to be in violation could be expelled from the NCAA. In 1950, seven schools, called the "Sinful Seven"—Virginia, Maryland, VMI, Virginia Tech, The Citadel, Boston College, and Villanova—admitted they were in violation of the code. Time magazine asserted violators were far more widespread than those seven that had confessed. Maryland was the only Sinful Seven school that was also a major football power with eighty scholarship players, and Byrd led them in their stand against the Sanity Code. University of Virginia president Colgate Darden called the code hypocritical, and The Citadel's leadership refused to "lie to stay in the association" and requested termination of its NCAA membership. At the convention to decide Virginia's fate, Byrd said, "Does Ohio State want to vote for expulsion of Virginia, when Ohio State has facilities to take care of four or five as many athletes as Virginia?" The ensuing vote fell 25 short of the needed two-thirds majority to expel the Sinful Seven.

In 1951, the football team's 10–0 season culminated in a 28–13 victory over first-ranked Tennessee in the 1952 Sugar Bowl. Maryland's participation, however, was in violation of a Southern Conference resolution passed mid-season that banned participation in postseason bowl games. Byrd had Maryland accept the bowl invitation, despite Tatum's objections. The coach thought the threatened sanctions, which prevented Maryland from playing any Southern Conference games the following season, would severely disadvantage his team. In 1952, Maryland and Clemson, which had also violated the bowl game ban, were sanctioned, and the incident hastened the break-up of the Southern Conference and formation of the Atlantic Coast Conference, of which both schools were founding members.

Opponents in The Baltimore Sun alleged that Byrd emphasized athletics over academics and belittled him as the only college football coach to rise to the position of university president. Among the campus expansions, Byrd was responsible for the construction of Byrd Stadium in 1950 and Cole Field House in 1955, which at the time was the largest basketball arena in the Southern Conference. Critics alleged that both facilities were constructed at the expense of campus libraries. Byrd also built the University of Maryland Golf Course in 1959. Byrd resigned from the post in 1953 and his tenure ended effectively on December 31.

## Political career

Byrd resigned from the presidency in January 1954 to embark upon an unsuccessful campaign for Governor of Maryland. He narrowly beat perennial candidate George P. Mahoney in the Democratic primary by 50.64% to 49.37% and faced Republican incumbent McKeldin in the general election. Byrd campaigned on his stance of separate but equal. McKeldin won comfortable majorities in Baltimore's black, Jewish, and upper-middle class white districts, while Byrd took all of the blue-collar white South and East Baltimore neighborhoods, including McKeldin's boyhood home along Eutaw Street. Elsewhere in the state, however, middle-class white voters did not support Byrd. Byrd lost by 54.46% to 45.54%. He went on to make unsuccessful bids for the Democratic nominations to the U.S. Senate in 1964 and the U.S. Congress in 1966.

Despite his lack of success in campaigning, Byrd did receive several gubernatorial appointments: Chairman of the Maryland Tidewater Fisheries Commission, Maryland Commissioner to the Potomac River Fisheries Commission, and Chairman of the Commission on Chesapeake Bay Affairs. In 1959, Governor J. Millard Tawes appointed Byrd as commissioner of tidewater fisheries. When a fisheries officer killed a Virginian waterman illegally dredging, Byrd disarmed the force. The action was credited with helping to end the long-standing Potomac River Oyster Wars. Following the example of other oyster-producing states, Byrd authorized fossil shell mining to produce culch, crushed shells used to form oyster beds. Byrd ignored Tawes' warning to "stay away from private planting" by promoting the formation of leasing cooperatives, but his plan failed due to opposition in the Maryland General Assembly.

## Business career

Byrd was also active in business and civic organizations. In 1951, he was involved in the merger that formed the Suburban Trust Company, which in 1960 was the largest bank in Maryland outside of Baltimore City. He later served as the company's vice president. Byrd also did business in real estate and construction. Byrd was active with service organizations. In 1962, he became a member of the Loyal Order of the Moose. Byrd organized the College Park Rotary Club and served as its first president. Byrd was a member of the Defense Orientation Conference Association (DOCA), an organization which educates civilians on the Defense Department's programs and policies.

## Death

Byrd died of a heart condition on October 2, 1970, at the University of Maryland Hospital in Baltimore, Maryland. He is interred at Asbury United Methodist Church Cemetery in Crisfield, Maryland, and his epitaph reads: "Harry Clifton 'Curley' Byrd, Educator–Statesman–Conservationist, President Emeritus, Father and Builder of the Greater Consolidated University of Maryland, Founded 1920." Byrd was inducted into the University of Maryland Athletic Hall of Fame in 1982.

## Head coaching record

### Football

### Baseball

Athlete, academic, and politician

George Washington Colonials football players

High school football coaches in Washington, D.C.

Maryland Terrapins men's track and field athletes

Maryland Terrapins track and field coaches

McDaniel Green Terror men's track and field athletes

Players of American football from Maryland

Presidents of the University of Maryland, College Park

University of Maryland, College Park faculty


Fishing Creek (North Branch Susquehanna River tributary)

Fishing Creek is a 29.98-mile (48.25 km) long tributary of the Susquehanna River in Columbia County, Pennsylvania, in the United States. It joins the Susquehanna River near the census-designated place of Rupert and the town of Bloomsburg. The watershed has an area of 385 square miles (1,000 km2).

Nomadic Native Americans arrived in the lower reaches of Fishing Creek around 8000 BCE, and some were spending winters in the upper reaches of the valley by 3000 to 2000 BCE. In the past few centuries, the Fishing Creek area has been home to many industries, mills, and dams. It drains parts of five Pennsylvania counties: Columbia, Montour, Sullivan, Luzerne, and Lycoming. The creek's main tributaries include Hemlock Creek, Little Fishing Creek, Green Creek, Huntington Creek, West Branch Fishing Creek, and East Branch Fishing Creek.

Public recreation activities include canoeing, birdwatching, and fishing. The creek is known for its trout population, which includes brook, brown and rainbow trout; it also contains many other species of fish. Northern hardwood trees and ruffed grouse live in the surrounding area.

Some stretches of Fishing Creek contain significant amounts of algae because of leaking septic systems in the watershed. The area around the tributary West Creek is the least habitable part of the Fishing Creek area, according to a 2011 study. The water quality of Fishing Creek can vary. Its pH ranges from 4.9 to 8.5, while the concentration of dissolved oxygen ranges from 5 to 17.5 mg per liter. The creek's average discharge is 615 cubic feet per second (17.4 m3/s); its watershed contains gravel, shale and various loams—in particular the Albrights soil series and the Leck Kill soil.

## Course

Fishing Creek's source is 920 feet (280 m) above sea level in Sugarloaf Township, south of State Game Lands Number 13 and Pennsylvania Route 118, where East Branch and West Branch Fishing Creeks of southern Sullivan County meet in northern Columbia County. The creek heads approximately south with a few bends through Sugarloaf Township for about 2 miles (3.2 km). In the southern part of the township, it turns east for less than a mile and picks up Coles Creek—its first named tributary after the confluence of the East and West Branches. It empties into Fishing Creek from the northeast, 26.34 miles (42.39 km) upstream of its mouth.

Around this point, Fishing Creek turns sharply south into Benton Township and starts flowing parallel to Pennsylvania Route 487. Here it flows four or five miles, including about a mile in Benton, where West Creek parallels Fishing Creek and empties into it from the west just south of Benton and 21.72 miles (34.95 km) upstream of the mouth. Fishing Creek crosses under Pennsylvania Route 239 and continues approximately south, passing through the community of Maple Grove and flowing into Fishing Creek Township and Stillwater. In Stillwater, Raven Creek empties into the creek from the northeast, 18.62 miles (29.97 km) above the mouth. About 1.5 to 2 miles (2.4–3.2 km) south, the creek turns and picks up Huntington Creek, and then flows past the communities of Zaners, Forks, and Pealertown. The mouth of Huntington Creek is 15.1 miles (24.3 km) above the mouth of Fishing Creek.

Upon leaving Fishing Creek Township, about 1 mile (1.6 km) after picking up Huntington Creek, Fishing Creek flows southwest past Knob Mountain and into Orange Township. It passes near the northern edge of Knob Mountain 2 miles (3.2 km) downstream, then by Orangeville, and makes a 90° turn to the northwest. Shortly after this turn it picks up Green Creek 10.84 miles (17.45 km) above its mouth and turns west. After some distance, it turns south again, passing Bowman Bridge and a gauging station. From this point, the creek flows along the border between Orange and Mount Pleasant Townships for almost 2 miles (3.2 km). While on the border between these two townships, it flows past Kocher Park. The creek stays considerably nearer to the western edge of the river valley than the eastern edge at this point. Near Lightstreet, it turns west into Mount Pleasant Township, passing several lakes and the Turkey Hill Oxbow. Upon entering Mount Pleasant Township, the creek stops paralleling Pennsylvania Route 487 and flows in the vicinity of Interstate 80 for 2 to 3 miles (3.2–4.8 km).

Along the border of Mount Pleasant Township and Bloomsburg, Fishing Creek picks up Little Fishing Creek at a distance of 3.86 miles (6.21 km) upstream of its mouth before turning south and paralleling the western border of Bloomsburg. As it flows between Bloomsburg and Fernville, it turns sharply westward, paralleling U.S. Route 11, and picks up Hemlock Creek, which is 1.52 miles (2.45 km) above the mouth. Shortly after picking up Hemlock Creek, Fishing Creek turns southeast under U.S. Route 11 and flows parallel to Pennsylvania Route 42 for slightly over 1 mile (1.6 km), picking up Montour Run from the right, then empties 0.72 miles (1.16 km) later into the Susquehanna between Bloomsburg and Rupert. The Rupert Covered Bridge No. 56 crosses the main stem of the creek. Its mouth is 456 feet (139 m) above sea level—464 feet (141 m) lower than, and 29.98 miles (48.25 km) downstream of, the source.

### Tributaries

Fishing Creek has several major tributaries and numerous minor ones. The major tributaries are Hemlock Creek, Little Fishing Creek, Green Creek, Huntington Creek, and the East and West Branch Fishing Creeks. West Branch Fishing Creek rises on North Mountain and flows east into Fishing Creek. East Branch Fishing Creek is a tributary that starts on North Mountain in Sullivan County and is approximately 4.4 miles (7.1 km) long. Huntington Creek starts in State Game Lands number 57 and heads southwest through Luzerne County until it reaches the north side of Knob Mountain, which it runs parallel to until it merges with Fishing Creek. Huntington Creek drains the eastern and northeastern parts of the Fishing Creek watershed. Four covered bridges cross Huntington Creek; these are the Twin Bridges–East Paden Covered Bridge No. 120, the Twin Bridges–West Paden Covered Bridge No. 121, the Josiah Hess Covered Bridge No. 122, and the Huntington Mills Bridge.

Green Creek rises near Waller and heads roughly south to Rohrsburg and on to Orangeville, where it joins Fishing Creek. It drains the central part of the Fishing Creek watershed. Little Fishing Creek starts just in Lycoming County near the Columbia County Line. It winds through rural areas before reaching Pennsylvania Route 42, which it runs parallel to for the remainder of its length. It drains the western part of the Fishing Creek watershed. Four covered bridges cross Little Fishing Creek; these are the Wanich Covered Bridge No. 69, the Sam Eckman Covered Bridge No. 92, the Jud Christie Covered Bridge No. 95, and the Creasyville Covered Bridge.

Other tributaries of the main stem include Coles Creek and West Creek near Benton, Raven Creek in Fishing Creek Township, Hemlock Creek in Hemlock Township, Montour Run in Montour Township, and Deerlick Run and Stony Brook, both near Orange Township.

## Watershed

Fishing Creek drains most of Columbia County north of the Susquehanna River except for an area in the eastern part of the county, which is drained by Briar Creek. It also drains southern Sullivan County and western Luzerne County. Minor tributaries drain small portions of Montour County and southeastern Lycoming County. The upper part of the watershed is 85 percent forest and 13 percent farmland. Near its source, the other two percent is residential; closer to Benton, the remainder is urban. The creek's drainage basin consists of a number of sub-watersheds. The largest ones are the Huntington Creek watershed, with an area of 114 square miles; the Little Fishing Creek watershed, with an area of 68.1 square miles; the Green Creek drainage basin, with an area of 36.9 square miles; and the West Branch Fishing Creek drainage basin, with an area of 32.9 square miles.

### Oxbow lake

Northern Bloomsburg and Scott Township include a small oxbow lake of Fishing Creek; the area around this lake is known as the Turkey Hill Oxbow. The lake is located between Interstate 80 and the forests on the side of Turkey Hill. The oxbow is on a flood plain and includes grasses, forested wetlands, and areas of open water. In wet periods of the year, the Turkey Hill Oxbow lake receives overflow from the waters of Fishing Creek while during dry periods it contains water in only a few places.

Most land around the oxbow is steep. It is covered by hemlock and hardwood forests, as well as skunk cabbage seeps. The forests around the lake also contain black birch, yellow birch, white oak, red oak, sugar maple, tulip poplar, and Norway maple, while the understory contains slippery elm, European privet, Japanese barberry, American elderberry, wild hydrangea, witch hazel, mountain laurel, ironwood, and the rare American yew. The American yew population was in significant decline by 2004 due to heavy grazing by deer.

There are numerous wildflower species in the uplands and rock outcroppings of the Turkey Hill Oxbow. These include white baneberry, northern maidenhair fern, spikenard, blue cohosh, foamflower, false Solomon's seal, purple trillium, and wild columbine. Animals inhabiting the areas surrounding the pools include pickerel frogs, green frogs, wood ducks, and snapping turtles. Plants in this location include broadleaf arrowhead, northern blueflag, manna grasses, water starwort, and several varieties of sedges. Japanese knotweed has been seen near Interstate 80 on the northern edges of the Turkey Hill Oxbow.

## History

### Native American settlement

Having first inhabited Pennsylvania between 16,000 and 10,000 BCE, nomadic Native Americans reached the area near the mouth of Fishing Creek by 8000 BCE. By 3000 to 2000 BCE, some of them were going into the Fishing Creek valley during the winter to hunt deer and bears and returning to the Susquehanna River in the summer, creating trade routes. There was no permanent habitation until 1000 BCE when some Native American villages were built at the mouth of Fishing Creek. The Native Americans who settled in this area included the Shawnee and Susquehannock Indians. A Native American path ran along the creek from Bloomsburg to Orangeville before turning away in the direction of Tunkhannock Creek. Since at least 1769, there has also been a path between the mouths of Huntington and Green Creeks.

### European settlement

The first lots at the mouth of Fishing Creek were surveyed in 1769 when European settlers began moving into the area, and in the same year, the Penn family purchased 1,060 acres (430 hectares) of land 2 miles (3.2 km) upstream of Benton. In 1778, Moses Van Campen built a fort of logs covered with earth with a small swivel cannon on Fishing Creek to protect settlers on the frontier. There were settlers on the creek in Orange Township in 1780, and the Fishing Creek valley north of Orangeville, in what is now Stillwater, was first settled in 1783 by Daniel McHenry. The headwaters of the creek were settled in the late 1780s and early 1790s. Leonard Rupert established a ferry on the creek in 1786. The first sawmill on the upper portion of Fishing Creek was built in the late 1790s; it was destroyed in a flood in 1848.

The first mill in Sugarloaf Township was built alongside Fishing Creek in 1802, and another mill in the same township was noted for its buckwheat flour. A schoolhouse had been built by 1806. In 1818, John Barton built a flour and grist mill on Fishing Creek. It was destroyed by fire in 1855 and again in 1905. Although rebuilt, it burned down again in 1932. Another gristmill stood on the creek until 1830 when it was converted into a paper mill. Iron ore was discovered in the area of Fishing Creek in 1822, and in 1844, an anthracite-burning furnace was built on the creek near Bloomsburg. In the 19th century, an aqueduct was built across the creek. From around 1840 to 1900, the wagon-making industry was important to the upper Fishing Creek area. Another historic industry was the Susquehanna Slate Company, which operated in the late 19th century. The Fishing Creek Confederacy (August–November 1864) during the American Civil War was a suspected uprising of a high number of deserters and draft evaders. A thousand soldiers occupied and searched the Fishing Creek valley and the mountains of its headwaters but were unable to find any deserters. Nevertheless, 100 residents of Columbia County were arrested and imprisoned for desertion and draft evasion although most were later released. Starting in 1877, the Bloomsburg Water Company used Fishing Creek as its water supply. The Bloomsburg and Sullivan Railroad, which paralleled the creek, was built in 1888.

There were limestone mines at the junction of Fishing Creek and Little Fishing Creek, but these have not been used since at least 1887. During the Great Depression, a beach was constructed on the creek near Fernville by the Works Progress Administration. After the creek flooded in 1972 from Hurricane Agnes, a flash flood warning system was installed there. In 2002, a tract of land from the Custer/Kocher homestead on Fishing Creek near Lightstreet was converted into a park called the Frank W. Kocher Memorial Park, which was later expanded to cover 7 acres (2.8 ha). In the 21st century, the only significant industry in the watershed is the Benton Foundry.

## Hydrology

Approximately 1 mile (1.6 km) downstream of Orangeville a gauging station was established on the creek in 1938. Other monitoring of the creek has included detailed studies at a stream-gauging station near Bloomsburg, which operated from 2002 to 2012.

### Discharge

Just downstream of Orangeville, Fishing Creek's discharge averages 615 cubic feet per second (17.4 m3/s), with a median of 361 cubic feet per second (10.2 m3/s). The lowest recorded discharge was 90 cubic feet per second (2.5 m3/s) while the highest was 2,580 cubic feet per second (73 m3/s). Further upstream in Benton, it is almost always less than 720 cubic feet per second (20 m3/s), and usually approaches zero during the summer. The typical discharge is around 540 cubic feet per second (15 m3/s). In years of drought, the streambeds of West Branch and East Branch Fishing Creeks typically run dry for 105 days over summer; even in wet years they are dry for an average of 5 days. Near Bloomsburg, Fishing Creek's discharge has ranged between 10 cubic feet per second (0.28 m3/s) and 5,350 cubic feet per second (151 m3/s).

### pH

Near Benton, Fishing Creek's pH ranges from around 5.6 to 7.25, while near Bloomsburg, a wider range has been recorded, from 5.8 to 8.5. Near Camp Lavigne, it ranges from 5.5 to 7.1. East Branch Fishing Creek is the only stream in the watershed whose pH drops below 5.5; it can fall as low as 4.9. West Creek and Coles Creek are the least acidic streams in the watershed, with pH levels usually above 6.3 and often above 7. Typically, the creek and its tributaries are not at risk of becoming too acidic for the optimal health of fish, but in early spring during snowmelts, the levels approach the limit that brook trout can tolerate. Fishing Creek's waters are acidic because of acid rain.

### Dissolved chemicals

#### Nonmetals

The concentration of dissolved oxygen in Fishing Creek ranges from approximately 5 to 17.5 mg/L at Benton. A site near Camp Lavigne had slightly less variability, ranging from 8 to 17 mg/L. The concentration near Bloomsburg ranged between 4.1 and 17.1 mg/L, with an average of 10.9 mg/L. The amount of carbon dioxide near Bloomsburg ranged from 0.3 to 34 mg/L, with an average of 2.04 mg/L.

The total concentration of nitrogen near Bloomsburg between 2002 and 2012 ranged from 0.52 to 2.8 mg/L. The average concentration was 1.212 mg/L. The ammonia levels in the creek ranged from less than 0.02 mg/L to 0.06 mg/L, while the concentration of nitrates was always less than 0.04 mg/L. The total concentration of phosphates ranged from less than 0.031 mg/L to 0.11 mg/L, while for phosphorus the figures ranged from less than 0.01 mg/L to 0.575 mg/L.

The total concentration of dissolved solids near Bloomsburg ranges from less than 2 to 166 mg/L.

#### Metals

In most places on Fishing Creek, there is not enough dissolved aluminum to be toxic, although East Branch Fishing Creek has aluminum concentrations of over 100 μg per liter, approaching a lethal level for fish. Fishing Creek itself and all its other tributaries have concentrations of less than 70 μg per liter. The concentration is seasonal: aluminum trapped in frozen ground is released into the streams when the soil thaws. As a result, aluminum levels in the creek peak in March and April and drop to almost zero in the summer.

The concentration of calcium at the gauging station near Bloomsburg has ranged from 5.5 mg/L to 26 mg/L, averaging 7.532 mg/L. The concentration of magnesium has ranged from 1.5 mg/L to 6.7 mg/L, with an average of 1.748 mg/L.

### Dams

There are five dams on Fishing Creek. The lowhead dam called Boone's Dam is the furthest downstream, in Montour Township. It is 4.5 feet (1.4 m) high and 253 feet (77 m) long. Further upstream is the Diverting Dam, a 2-foot (0.6-meter) high and 100-foot (31-meter) long dam in Bloomsburg. It was built to power the nearby Irondale furnaces. A 380-foot (120 m) wide and 5-foot (1.5 m) high unnamed dam is on the creek further upstream, in Mount Pleasant Township. The uppermost dams are the 130-foot (40 m) wide and 11-foot (3.4 m) high Benton Dam and the 150-foot (46 m) wide and 6-foot (1.8 m) high Mill Dam, which are in Benton Township and Benton. Additionally, the Jonestown Dam is on the tributary Huntington Creek in Jonestown. This dam is 8 feet (2.4 m) high and 120 feet (37 m) wide.

### Water temperature

The highest water temperature is at West Creek, which can reach 77 °F (25 °C) in the summer. In Benton, Fishing Creek can reach 75 °F (24 °C) in the summer while Coles Creek only reaches 66 to 68 °F (19 to 20 °C). In the winter, the water in the main stem is around 32 °F (0 °C), while in West Branch Fishing Creek it can drop to 28 °F (−2 °C) in the winter, making it the coldest stream in the watershed. At the gauging station near Bloomsburg, the temperature has ranged from 32 to 78 °F (0 to 26 °C); it was at its lowest on January 10, 2011. The highest temperature occurred on August 3, 2006. The average temperature in August was 72.81 °F (22.67 °C) and the average water temperature in January was 35.46 °F (1.92 °C). The temperature has averaged approximately 53.65 °F (12.03 °C).

## Geology

The Fishing Creek watershed has been affected by glaciation, which has left a glacial till near the source and glacial outwash in the lower parts of the watershed. The watershed lies in two major geological regions: the Deep Valley section of the Allegheny Plateau and the Susquehanna Lowlands Section. The Allegheny Plateau lies in the upper reaches of the watershed and is characterized by deep valleys and rounded mountains with elevations of around 2,400 feet (730 m). The Susquehanna Lowlands section is characterized by linear ridges of moderate elevation and valleys less steep than those of the Deep Valley region. There are also flood plains along the creek. Near its mouth, it cuts through Montour Ridge, and a basalt-containing section of the Catskill Formation extends to the creek's banks in Hemlock Township. Other rock formations along the banks include the Clinton Formation, the Selena Formation, the Lower Helderburg Formation, and the Hamilton Formation. There is a terminal moraine, which crosses the creek near Benton.

The bed of Fishing Creek contains red and brown shale in some places. Other parts of the watershed lie over gray sandstone or conglomerates. There are numerous deposits of iron ore, limestone and marble in the watershed of Fishing Creek. Most of the rock in the watershed, including the Trimmers Rock Formation and Catskill Formation, is from the Devonian Period, but some of the northernmost tributaries have watersheds on rock from the Mississippian Period, such as the Huntley Mountain Formation and Burgoon sandstone. The creek is a freestone stream although its water is colder than that of most eastern freestone streams.

Areas along Fishing Creek contain pools followed by riffles, which are further followed by more pools. This configuration of pools and riffles creates an ideal situation for fly-fishing. The lower part of the creek forms one side of a triangle of low-lying land in western Bloomsburg, which floods severely during heavy rains.

### Soil

The main soil in the area of Fishing Creek belongs to the Albrights series, which contains a 7-inch (18 cm) layer of sticky, reddish-brown, gravelly silt loam. Below this is a layer of yellowish-red, gravelly, silty clay loam, which extends to approximately 30 inches (76 cm) below ground and lies over a layer of equal portions of gravel and silty clay loam. Bedrock occurs several feet below the surface. The top 8 inches (20 cm) of the Leck Kill-Meckesville-Calvin series in the watershed is dark brown silt loam with small pieces of sandstone and shale. A subsoil of reddish-brown silt loam from 8 to 32 inches (20 to 81 cm) below ground is followed by a 6-inch (15 cm) layer of sticky clay loam, below which is a bedrock of red shale.

The Barbour series occurs near the source of the creek. It is topped with a crumbly, 10-inch (25 cm) layer of brownish-red silt loam over a loose subsoil of reddish-brown loam with some gravel. The top layer can easily be penetrated by roots and water. Further down is a layer of reddish-brown gravel and sand, which extends to 10 feet (3.0 m) or more underground. The Basher series also occurs along upper Fishing Creek. The top layer is a loose, crumbly, reddish-brown sandy loam extending to 9 inches (23 cm) underground, and the subsoil is a loose, porous, reddish-brown sandy loam with some gravel, extending to 20 inches (51 cm) underground. Lower down, there is a layer of red sandy loam with some gravel that extends from 15 to 30 inches (38 to 76 cm) underground.

The Pekin series is found along Fishing Creek and its tributary Huntington Creek. The uppermost layer, a dark brown silt loam that extends to 8 inches (20 cm) underground, lies over a layer of brown silt loam with 10 percent gravel extending 16 inches (41 cm) underground. The subsoil is mottled, brown, silty clay loam with cobbles and extends to 40 inches (100 cm) underground. Bedrock occurs at a depth of 6 to 40 feet (1.8 to 12.2 m) underground. The Pekin soils near the creek contain more cobbles than typical Pekin soils. Soils of the Chen1ango-Pope-Holly series have also been found along it.

In 1914 the soils of the Fishing Creek watershed were found to yield large quantities of farm crops. Potatoes yielded 100 to 200 bushels per acre, corn 70 to 90 bushels per acre, oats 40 bushels per acre, wheat 20 to 30 bushels per acre, and hay one to two tons per acre. J. H. Battle's 1887 History of Columbia and Montour Counties, Pennsylvania stated that the Fishing Creek valley was fertile.

## Biology

Benthic algae densely cover the bed of Fishing Creek, their preponderance attributed to leaking septic systems. At one location on the main stem downstream of Grassmere Park, coverage exceeds 60 percent. The dominant algal organism on West Branch Fishing Creek near the village of Elk Grove is Cladophora. The green algae Tetraspora dominates the stretch of Fishing Creek for 3 miles (4.8 km) downstream of Grassmere Park, where it covers 80 percent of the riverbed. South of Pennsylvania Route 239's crossing of the creek, the dominant algal organisms are Microspora, Mougeotia, and Spirogyra. In the fall, decomposing algae covers 50 percent of the riverbed.

Thirty-six species of macroinvertebrates live in Fishing Creek. The highest level of macroinvertebrate biodiversity on upper Fishing Creek is near Grassmere Park while the lowest is in Benton. The number of these organisms per square meter on Fishing Creek ranges from under 200 in Benton to nearly 400 halfway between Coles Creek and Benton. The highest density of them in the watershed occurs at West Creek where there are between 600 and almost 900 per m2 and the lowest density occurs at a site on East Branch Fishing Creek, where there are approximately 100 per m2.

Some of Fishing Creek is stocked by the Fishing Creek Sportsman's Association and contains populations of brook trout, rainbow trout, and brown trout. Many of them are sizable; the largest one caught in Fishing Creek weighed 8 pounds (3.6 kg) and was 28 inches (71 cm) long. All streams in the watershed are suitable for trout habitation according to the Pennsylvania Fish and Boat Commission. An 1887 book stated that Fishing Creek and its tributaries may have once been "alive with trout". In the upper part of the watershed, wild brook trout are most common in West Branch Fishing Creek and fish in general are least common in East Branch Fishing Creek. West Creek has higher fish diversity than any other stream in the upper part of the watershed and is also the only place that is inhabited by wild brown trout. In addition, sculpin and cutlips minnow have been observed in large numbers in the creek and its tributaries. Less commonly observed fish in the upper part of the watershed include johnny darters, white suckers, and black-nosed dace. It is difficult for fish to spawn in the creek because of poor water quality near Benton, a lack of food, and dry headwaters for part of the year. The fish diversity in East Branch Fishing Creek and West Branch Fishing Creek is also significantly affected by episodic acidification, which is caused by acid rain falling in areas with no limestone in the bedrock. The main stem experiences similar problems but to a lesser extent, and the tributaries Coles Creek and West Creek experience the problems even less.

Northern hardwood trees are common in the Fishing Creek watershed. Ruffed grouse are common along Little Fishing Creek and its tributaries north of Iola. There are populations of Japanese knotweed, an invasive plant, along the creek and its tributaries south of Pennsylvania Route 118.

### Habitat quality

In 2011, the habitat quality of upper Fishing Creek and its tributaries were rated on a scale of 1 to 200 (with a higher rating indicating better habitability) by Point Park University and the Fishing Creek Sportsmans' Association. Most of this part of the creek and its tributaries were rated 166 or higher, which was considered optimal. The waters near the mouths of West Branch and East Branch Fishing Creeks, and Fishing Creek near Benton, were rated 113 to 160, considered suboptimal. A portion of West Creek was rated 60–112, considered marginal.

The highest Shannon Diversity Index of any stream in the Fishing Creek watershed is around 2.75, for West Branch Fishing Creek. This value is closely followed by that of West Creek, which has an index of 2.5 to 2.6. The lowest value in the watershed is that of East Branch Fishing Creek, which is around 1.2. The main stem has a Shannon Diversity Index of 2.1 to 2.4, depending on the site.

The Fishing Creek Sportsmans' Association has proposed a number of methods to conserve Fishing Creek and its tributaries. These include planting riparian buffers, eliminating leaky septic systems, and protecting the area from hydraulic fracturing.

## Recreation

The Fishing Creek Watershed Association plans to open a public section of the creek that stretches for 6,500 feet (2,000 meters), with a park of 92 acres (37.2 ha). There are other tracts of public property along the creek, one of which, called the Power Dam, is 2 miles (3.2 km) upstream of Benton. It covers 19 acres (7.7 ha) and stretches for 2,900 feet (880 meters) of Fishing Creek, and contains the remains of a concrete dam. Another public area is the Benton Overlook 1 mile (1.6 km) into Benton, which covers 42 acres (17.0 ha) and stretches for 2,600 feet (790 meters) near the creek. A public site at the Zaners Bridge in Zaner 2.5 miles (4.0 km) downstream from Stillwater covers 31 acres (12.5 ha) along about 1,000 feet (300 meters) of the creek and contains an abandoned railroad grade.

The Grassmere Park Campground was established in the early 1900s on Fishing Creek. Further downstream, near Lightstreet, is Kocher Park, which occupies more than 7 acres (2.8 ha). Typical activities there include canoeing, dog walking, birdwatching and fishing.

The western part of Pennsylvania State Game Lands Number 13 is in a gorge cut by West Branch Fishing Creek. These state game lands have an area of 50,000 acres and feature many forest roads and old grades. The hiking trail Waterfall Wonderland, which affords views of Big, Twin, Lewis, and Sullivan Falls, is described as "a place of almost mystical beauty" by Jeff Mitchell in his book Hiking the Endless Mountains: Exploring the Wilderness of Northeastern Pennsylvania. The state game lands are less crowded than the nearby Ricketts Glen State Park.

The Jakey Hollow Natural Area is on a small tributary of Little Fishing Creek. It is near Mordansville and features old-growth forests. The natural area is one of the smallest in Pennsylvania.

## See also

- Corn Run, next tributary of the Susquehanna River going downriver
- Kinney Run, next tributary of the Susquehanna River going upriver
- List of rivers of Pennsylvania

Tributary of river in Pennsylvania

Canoeing and kayaking venues in the United States

Recreational fishing in the United States

Tributaries of Fishing Creek (North Branch Susquehanna River)


Structural alignment

Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.

Structural alignments can compare two sequences or multiple sequences. Because these alignments rely on information about all the query sequences' three-dimensional conformations, the method can only be used on sequences where these structures are known. These are usually found by X-ray crystallography or NMR spectroscopy. It is possible to perform a structural alignment on structures produced by structure prediction methods. Indeed, evaluating such predictions often requires a structural alignment between the model and the true known structure to assess the model's quality. Structural alignments are especially useful in analyzing data from structural genomics and proteomics efforts, and they can be used as comparison points to evaluate alignments produced by purely sequence-based bioinformatics methods.

The outputs of a structural alignment are a superposition of the atomic coordinate sets and a minimal root mean square deviation (RMSD) between the structures. The RMSD of two aligned structures indicates their divergence from one another. Structural alignment can be complicated by the existence of multiple protein domains within one or more of the input structures, because changes in relative orientation of the domains between two structures to be aligned can artificially inflate the RMSD.

## Data produced by structural alignment

The minimum information produced from a successful structural alignment is a set of residues that are considered equivalent between the structures. This set of equivalences is then typically used to superpose the three-dimensional coordinates for each input structure. (Note that one input element may be fixed as a reference and therefore its superposed coordinates do not change.) The fitted structures can be used to calculate mutual RMSD values, as well as other more sophisticated measures of structural similarity such as the global distance test (GDT, the metric used in CASP). The structural alignment also implies a corresponding one-dimensional sequence alignment from which a sequence identity, or the percentage of residues that are identical between the input structures, can be calculated as a measure of how closely the two sequences are related.

## Types of comparisons

Because protein structures are composed of amino acids whose side chains are linked by a common protein backbone, a number of different possible subsets of the atoms that make up a protein macromolecule can be used in producing a structural alignment and calculating the corresponding RMSD values. When aligning structures with very different sequences, the side chain atoms generally are not taken into account because their identities differ between many aligned residues. For this reason it is common for structural alignment methods to use by default only the backbone atoms included in the peptide bond. For simplicity and efficiency, often only the alpha carbon positions are considered, since the peptide bond has a minimally variant planar conformation. Only when the structures to be aligned are highly similar or even identical is it meaningful to align side-chain atom positions, in which case the RMSD reflects not only the conformation of the protein backbone but also the rotameric states of the side chains. Other comparison criteria that reduce noise and bolster positive matches include secondary structure assignment, native contact maps or residue interaction patterns, measures of side chain packing, and measures of hydrogen bond retention.

### Structural superposition

The most basic possible comparison between protein structures makes no attempt to align the input structures and requires a precalculated alignment as input to determine which of the residues in the sequence are intended to be considered in the RMSD calculation. Structural superposition is commonly used to compare multiple conformations of the same protein (in which case no alignment is necessary, since the sequences are the same) and to evaluate the quality of alignments produced using only sequence information between two or more sequences whose structures are known. This method traditionally uses a simple least-squares fitting algorithm, in which the optimal rotations and translations are found by minimizing the sum of the squared distances among all structures in the superposition. More recently, maximum likelihood and Bayesian methods have greatly increased the accuracy of the estimated rotations, translations, and covariance matrices for the superposition.

Algorithms based on multidimensional rotations and modified quaternions have been developed to identify topological relationships between protein structures without the need for a predetermined alignment. Such algorithms have successfully identified canonical folds such as the four-helix bundle. The SuperPose method is sufficiently extensible to correct for relative domain rotations and other structural pitfalls.

### Evaluating similarity

Often the purpose of seeking a structural superposition is not so much the superposition itself, but an evaluation of the similarity of two structures or a confidence in a remote alignment. A subtle but important distinction from maximal structural superposition is the conversion of an alignment to a meaningful similarity score. Most methods output some sort of "score" indicating the quality of the superposition. However, what one actually wants is not merely an estimated "Z-score" or an estimated E-value of seeing the observed superposition by chance but instead one desires that the estimated E-value is tightly correlation to the true E-value. Critically, even if a method's estimated E-value is precisely correct on average, if it lacks a low standard deviation on its estimated value generation process, then the rank ordering of the relative similarities of a query protein to a comparison set will rarely agree with the "true" ordering.

Different methods will superimpose different numbers of residues because they use different quality assurances and different definitions of "overlap"; some only include residues meeting multiple local and global superposition criteria and others are more greedy, flexible, and promiscuous. A greater number of atoms superposed can mean more similarity but it may not always produce the best E-value quantifying the unlikeliness of the superposition and thus not as useful for assessing similarity, especially in remote homologs.

## Algorithmic complexity

### Optimal solution

The optimal "threading" of a protein sequence onto a known structure and the production of an optimal multiple sequence alignment have been shown to be NP-complete. However, this does not imply that the structural alignment problem is NP-complete. Strictly speaking, an optimal solution to the protein structure alignment problem is only known for certain protein structure similarity measures, such as the measures used in protein structure prediction experiments, GDT_TS and MaxSub. These measures can be rigorously optimized using an algorithm capable of maximizing the number of atoms in two proteins that can be superimposed under a predefined distance cutoff. Unfortunately, the algorithm for optimal solution is not practical, since its running time depends not only on the lengths but also on the intrinsic geometry of input proteins.

### Approximate solution

Approximate polynomial-time algorithms for structural alignment that produce a family of "optimal" solutions within an approximation parameter for a given scoring function have been developed. Although these algorithms theoretically classify the approximate protein structure alignment problem as "tractable", they are still computationally too expensive for large-scale protein structure analysis. As a consequence, practical algorithms that converge to the global solutions of the alignment, given a scoring function, do not exist. Most algorithms are, therefore, heuristic, but algorithms that guarantee the convergence to at least local maximizers of the scoring functions, and are practical, have been developed.

## Representation of structures

Protein structures have to be represented in some coordinate-independent space to make them comparable. This is typically achieved by constructing a sequence-to-sequence matrix or series of matrices that encompass comparative metrics: rather than absolute distances relative to a fixed coordinate space. An intuitive representation is the distance matrix, which is a two-dimensional matrix containing all pairwise distances between some subset of the atoms in each structure (such as the alpha carbons). The matrix increases in dimensionality as the number of structures to be simultaneously aligned increases. Reducing the protein to a coarse metric such as secondary structure elements (SSEs) or structural fragments can also produce sensible alignments, despite the loss of information from discarding distances, as noise is also discarded. Choosing a representation to facilitate computation is critical to developing an efficient alignment mechanism.

## Methods

Structural alignment techniques have been used in comparing individual structures or sets of structures as well as in the production of "all-to-all" comparison databases that measure the divergence between every pair of structures present in the Protein Data Bank (PDB). Such databases are used to classify proteins by their fold.

### DALI

A common and popular structural alignment method is the DALI, or Distance-matrix ALIgnment method, which breaks the input structures into hexapeptide fragments and calculates a distance matrix by evaluating the contact patterns between successive fragments. Secondary structure features that involve residues that are contiguous in sequence appear on the matrix's main diagonal; other diagonals in the matrix reflect spatial contacts between residues that are not near each other in the sequence. When these diagonals are parallel to the main diagonal, the features they represent are parallel; when they are perpendicular, their features are antiparallel. This representation is memory-intensive because the features in the square matrix are symmetrical (and thus redundant) about the main diagonal.

When two proteins' distance matrices share the same or similar features in approximately the same positions, they can be said to have similar folds with similar-length loops connecting their secondary structure elements. DALI's actual alignment process requires a similarity search after the two proteins' distance matrices are built; this is normally conducted via a series of overlapping submatrices of size 6x6. Submatrix matches are then reassembled into a final alignment via a standard score-maximization algorithm — the original version of DALI used a Monte Carlo simulation to maximize a structural similarity score that is a function of the distances between putative corresponding atoms. In particular, more distant atoms within corresponding features are exponentially downweighted to reduce the effects of noise introduced by loop mobility, helix torsions, and other minor structural variations. Because DALI relies on an all-to-all distance matrix, it can account for the possibility that structurally aligned features might appear in different orders within the two sequences being compared.

The DALI method has also been used to construct a database known as FSSP (Fold classification based on Structure-Structure alignment of Proteins, or Families of Structurally Similar Proteins) in which all known protein structures are aligned with each other to determine their structural neighbors and fold classification. There is an searchable database based on DALI as well as a downloadable program and web search based on a standalone version known as DaliLite.

### Combinatorial extension

The combinatorial extension (CE) method is similar to DALI in that it too breaks each structure in the query set into a series of fragments that it then attempts to reassemble into a complete alignment. A series of pairwise combinations of fragments called aligned fragment pairs, or AFPs, are used to define a similarity matrix through which an optimal path is generated to identify the final alignment. Only AFPs that meet given criteria for local similarity are included in the matrix as a means of reducing the necessary search space and thereby increasing efficiency. A number of similarity metrics are possible; the original definition of the CE method included only structural superpositions and inter-residue distances but has since been expanded to include local environmental properties such as secondary structure, solvent exposure, hydrogen-bonding patterns, and dihedral angles.

An alignment path is calculated as the optimal path through the similarity matrix by linearly progressing through the sequences and extending the alignment with the next possible high-scoring AFP pair. The initial AFP pair that nucleates the alignment can occur at any point in the sequence matrix. Extensions then proceed with the next AFP that meets given distance criteria restricting the alignment to low gap sizes. The size of each AFP and the maximum gap size are required input parameters but are usually set to empirically determined values of 8 and 30 respectively. Like DALI and SSAP, CE has been used to construct an all-to-all fold classification database from the known protein structures in the PDB.

The RCSB PDB has recently released an updated version of CE, Mammoth, and FATCAT as part of the RCSB PDB Protein Comparison Tool. It provides a new variation of CE that can detect circular permutations in protein structures.

### Mammoth

MAMMOTH approaches the alignment problem from a different objective than almost all other methods. Rather than trying to find an alignment that maximally superimposes the largest number of residues, it seeks the subset of the structural alignment least likely to occur by chance. To do this it marks a local motif alignment with flags to indicate which residues simultaneously satisfy more stringent criteria: 1) Local structure overlap 2) regular secondary structure 3) 3D-superposition 4) same ordering in primary sequence. It converts the statistics of the number of residues with high-confidence matches and the size of the protein to compute an Expectation value for the outcome by chance. It excels at matching remote homologs, particularly structures generated by ab initio structure prediction to structure families such as SCOP, because it emphasizes extracting a statistically reliable sub alignment and not in achieving the maximal sequence alignment or maximal 3D superposition.

For every overlapping window of 7 consecutive residues it computes the set of displacement direction unit vectors between adjacent C-alpha residues. All-against-all local motifs are compared based on the URMS score. These values becomes the pair alignment score entries for dynamic programming which produces a seed pair-wise residue alignment. The second phase uses a modified MaxSub algorithm: a single 7 reside aligned pair in each proteins is used to orient the two full length protein structures to maximally superimpose these just these 7 C-alpha, then in this orientation it scans for any additional aligned pairs that are close in 3D. It re-orients the structures to superimpose this expanded set and iterates until no more pairs coincide in 3D. This process is restarted for every 7 residue window in the seed alignment. The output is the maximal number of atoms found from any of these initial seeds. This statistic is converted to a calibrated E-value for the similarity of the proteins.

Mammoth makes no attempt to re-iterate the initial alignment or extend the high quality sub-subset. Therefore, the seed alignment it displays can't be fairly compared to DALI or TM align as it was formed simply as a heuristic to prune the search space. (It can be used if one wants an alignment based solely on local structure-motif similarity agnostic of long range rigid body atomic alignment.) Because of that same parsimony, it is well over ten times faster than DALI, CE and TM-align. It is often used in conjunction with these slower tools to pre-screen large data bases to extract the just the best E-value related structures for more exhaustive superposition or expensive calculations.

It has been particularly successful at analyzing "decoy" structures from ab initio structure prediction. These decoys are notorious for getting local fragment motif structure correct, and forming some kernels of correct 3D tertiary structure but getting the full length tertiary structure wrong. In this twilight remote homology regime, Mammoth's e-values for the CASP protein structure prediction evaluation have been shown to be significantly more correlated with human ranking than SSAP or DALI. Mammoths ability to extract the multi-criteria partial overlaps with proteins of known structure and rank these with proper E-values, combined with its speed facilitates scanning vast numbers of decoy models against the PDB data base for identifying the most likely correct decoys based on their remote homology to known proteins.

### SSAP

The SSAP (Sequential Structure Alignment Program) method uses double dynamic programming to produce a structural alignment based on atom-to-atom vectors in structure space. Instead of the alpha carbons typically used in structural alignment, SSAP constructs its vectors from the beta carbons for all residues except glycine, a method which thus takes into account the rotameric state of each residue as well as its location along the backbone. SSAP works by first constructing a series of inter-residue distance vectors between each residue and its nearest non-contiguous neighbors on each protein. A series of matrices are then constructed containing the vector differences between neighbors for each pair of residues for which vectors were constructed. Dynamic programming applied to each resulting matrix determines a series of optimal local alignments which are then summed into a "summary" matrix to which dynamic programming is applied again to determine the overall structural alignment.

SSAP originally produced only pairwise alignments but has since been extended to multiple alignments as well. It has been applied in an all-to-all fashion to produce a hierarchical fold classification scheme known as CATH (Class, Architecture, Topology, Homology), which has been used to construct the CATH Protein Structure Classification database.

## Recent developments

Improvements in structural alignment methods constitute an active area of research, and new or modified methods are often proposed that are claimed to offer advantages over the older and more widely distributed techniques. A recent example, TM-align, uses a novel method for weighting its distance matrix, to which standard dynamic programming is then applied. The weighting is proposed to accelerate the convergence of dynamic programming and correct for effects arising from alignment lengths. In a benchmarking study, TM-align has been reported to improve in both speed and accuracy over DALI and CE.

Other promising methods of structural alignment are local structural alignment methods. These provide comparison of pre-selected parts of proteins (e.g. binding sites, user-defined structural motifs) against binding sites or whole-protein structural databases. The MultiBind and MAPPIS servers allow the identification of common spatial arrangements of physicochemical properties such as H-bond donor, acceptor, aliphatic, aromatic or hydrophobic in a set of user provided protein binding sites defined by interactions with small molecules (MultiBind) or in a set of user-provided protein–protein interfaces (MAPPIS). Others provide comparison of entire protein structures against a number of user submitted structures or against a large database of protein structures in reasonable time (ProBiS). Unlike global alignment approaches, local structural alignment approaches are suited to detection of locally conserved patterns of functional groups, which often appear in binding sites and have significant involvement in ligand binding. As an example, comparing G-Losa, a local structure alignment tool, with TM-align, a global structure alignment based method. While G-Losa predicts drug-like ligands’ positions in single-chain protein targets more precisely than TM-align, the overall success rate of TM-align is better.

However, as algorithmic improvements and computer performance have erased purely technical deficiencies in older approaches, it has become clear that there is no one universal criterion for the 'optimal' structural alignment. TM-align, for instance, is particularly robust in quantifying comparisons between sets of proteins with great disparities in sequence lengths, but it only indirectly captures hydrogen bonding or secondary structure order conservation which might be better metrics for alignment of evolutionarily related proteins. Thus recent developments have focused on optimizing particular attributes such as speed, quantification of scores, correlation to alternative gold standards, or tolerance of imperfection in structural data or ab initio structural models. An alternative methodology that is gaining popularity is to use the consensus of various methods to ascertain proteins structural similarities.

## RNA structural alignment

Structural alignment techniques have traditionally been applied exclusively to proteins, as the primary biological macromolecules that assume characteristic three-dimensional structures. However, large RNA molecules also form characteristic tertiary structures, which are mediated primarily by hydrogen bonds formed between base pairs as well as base stacking. Functionally similar noncoding RNA molecules can be especially difficult to extract from genomics data because structure is more strongly conserved than sequence in RNA as well as in proteins, and the more limited alphabet of RNA decreases the information content of any given nucleotide at any given position.

However, because of the increasing interest in RNA structures and because of the growth of the number of experimentally determined 3D RNA structures, few RNA structure similarity methods have been developed recently. One of those methods is, e.g., SETTER which decomposes each RNA structure into smaller parts called general secondary structure units (GSSUs). GSSUs are subsequently aligned and these partial alignments are merged into the final RNA structure alignment and scored. The method has been implemented into the SETTER webserver.

A recent method for pairwise structural alignment of RNA sequences with low sequence identity has been published and implemented in the program FOLDALIGN. However, this method is not truly analogous to protein structural alignment techniques because it computationally predicts the structures of the RNA input sequences rather than requiring experimentally determined structures as input. Although computational prediction of the protein folding process has not been particularly successful to date, RNA structures without pseudoknots can often be sensibly predicted using free energy-based scoring methods that account for base pairing and stacking.

## Software

Choosing a software tool for structural alignment can be a challenge due to the large variety of available packages that differ significantly in methodology and reliability. A partial solution to this problem was presented in and made publicly accessible through the ProCKSI webserver. A more complete list of currently available and freely distributed structural alignment software can be found in structural alignment software.

Properties of some structural alignment servers and software packages are summarized and tested with examples at Structural Alignment Tools in Proteopedia.Org.

## See also

- Multiple sequence alignment
- List of sequence alignment software
- Structural Classification of Proteins
- SuperPose
- Protein superfamily

Aligning molecular sequences using sequence and structural information