protein phosphorylation - mediated signal transduction is an important post - translational modification ( ptm)-based regulatory mechanism , and is implicated in a broad spectrum of key cellular molecular processes , including cell cycle , oncogenic transformation , immunological responsiveness , apoptosis and development ( 15 ) . in these activities ,
 phosphoprotein - binding domains ( ppbds , denoting domains that have specific binding affinity to phosphorylated sites in proteins ) play a pivotal role in connecting the kinases and the effector molecules , forming multi - protein complexes , and inducing specific protein 
protein interactions responsible for changes in these proteins subcellular localization , folding state , binding specificity or activity ( 6 ) .
ppbds achieve their binding specificity to their substrate proteins primarily through the recognition of a phosphopeptide ( ppep ) region , which are short peptide sequences ( 615 residues ) containing phosphorylated residues ( i.e. ps , pt or py , where s is serine , t is threonine and y is tyrosine ) ( 1,7 ) .
other factors , such as the tertiary structures , subcellular localization of the substrate proteins , as well as domain competition , are also known to influence ppbd 
phosphorylation sites are frequently found in intrinsically disordered or unstructured regions of the proteins ( 911 ) , making these regions good candidate sites for ppbd binding . in the human proteome ,
10 protein domains14 - 3 - 3 , brct , c2 , fha , mh2 , pbd , ptb , sh2 , wd-40 and ww  have been identified as ppbds , i.e. they possess phosphoprotein or ppep - binding activities ( table 1 ) . 

table 1.summary of the 10 human ppbd classesppbd ( class name)reported substrate specificityrefs.14 - 3 - 3r - s - x - ps - x - p , r - x - x - x - ps - x - p(1,20)brctps - x - x - f(21,22)c2(y / f)-(s / a)-(v / i)-py-(q / r)-x-(y / f)-x(23)fha ( forkhead - associated)pt - x - x - d(24,25)mh2 ( mad homology 2)ps - x - ps(26)pbd ( polo - box domain)s-(pt / ps)-(p / x)(27)ptb ( phosphotyrosine binding)n - p - x - py , n - p - x - y(28)sh2 ( src homology 2)py - x - x-(i / p ) ( crk ) ; py-(i / v / l)-x-(i / v / l ) ( ptpn11 ) ; py-(m / i / l / v / e)-x - m ( pik3r1)(29,30)wd-40d - ps - g--x - ps ( btrc ) ; ( i / l / p)-(i / l / p)-pt - p ( fbxw7)(31,32)ww(a / p)-p - p-(a / p)-y ; ps - p ; pt - p(33)the listed information is representative of the vast amount of literature information.the information also includes our unpublished data on sh2-ppep microarray data .
summary of the 10 human ppbd classes the listed information is representative of the vast amount of literature information .
the interactions between ppbds and their ppep substrates have been studied extensively using a variety of techniques , including structural determination ( using x - ray crystallography or nmr spectroscopy ) , peptide assay ( using phage display , synthetic peptide library or oriented peptide library ) , combinatorial screening , mass spectrometry analysis , mutagenesis ( usually followed by gst pull - down or yeast two - hybrid assays ) and computational sequence analysis ( 3 ) .
the rich information generated by these means is now partially captured by a few database resources , where the information about ppbds , ppbd - containing proteins and their interactions with ppep - containing substrate proteins can be obtained .
protein interaction databases such as bind ( 12 ) , hprd ( 13 ) and domino ( 14 ) , functional motif databases such as elm ( 8) and phospho.elm ( 15 ) , and a specialized prediction server  scansite , which makes predictions about the ppbd  ppep interactions based on results obtained from oriented peptide library experiments ( 16 ) . despite the availability of these existing resources ,
a database that offers integrated , comprehensive , detailed annotations regarding the proteomic interactions mediated by ppbds is still lacking .
pepcyber : ppep was constructed with the intention of filling this gap . in pepcyber : ppep , the information about ppbd - mediated protein interactions was carefully compiled through curation of peer - reviewed publications , and deposited into a relational database . for each interaction , specific information about the ppbd , ppbd - containing protein , the specific ppep substrate bound , the substrate protein , the evidence of the interaction and the citations were recorded .
moreover , information regarding the signaling pathways associated with the ppbd  ppep - binding interactions ( in particular , tumorigenesis - related signaling pathways and tumor types ) is also documented and stored in the database .
the data hosted in pepcyber : ppep meet the human proteome organization ( hupo ) , proteomics standards initiative ( psi ) standard ( 17 ) , which is supported by most major protein 
ppbd instance , and the collection of similar ppbd instances with a high level of sequence homology and structural similarity a 
ppbd class. for example , the sh2 domain located close to the n - terminus of the protein , ptpn11 ( shp2 ) , is an 
ppbd class. presently , there are 10 reported human ppbd classes ( table 1 ) .
the current pepcyber : ppep release ( v.1.0 , release 31 july 2007 ) includes 7044 ppbd - mediated interactions involving 337 ppbd - containing proteins and 1123 substrate proteins .
this rich information was obtained through the curation of 2446 peer - reviewed research articles published between 1975 and 2007 .
the largest number of interactions involves the sh2 ppbd class ( 4290 interactions ) that is followed by the ww ppbd class ( 1389 interactions ) and 14 - 3 - 3 ppbd class ( 1086 interactions ) .
these interactions were classified into three categories based on whether the interaction was known to be mediated by a concerned ppbd instance , and whether the substrate peptide had been identified : if the interaction was known to be mediated by a ppbd instance and the substrate peptide had been identified , the interaction was classified as  category a ; if the interaction was known to be mediated by a ppbd instance but the substrate peptide had not been identified , the interaction is classified as  category b ; if it was not known whether the interaction was mediated by a ppbd instance ( though one of the interacting proteins was a ppbd protein ) , then the interaction was classified as  category c. among the 7044 interactions documented in the current release of pepcyber : ppep , 5376 ( 76% ) are category a interactions .
the 14 - 3 - 3 , ptb and ww ppbd classes are unique in that they are also capable of binding to non - ppep substrates in certain instances .
there are a total of 1068 non - ppep interactions , accounting for 15% of the total collection of the current pepcyber : ppep release .
all non - ppep interactions documented are category a interactions . the web interface of the pepcyber : ppep database can be accessed through the url http://www.pepcyber.org / ppep/. five tabs are located underneath the logo of the web site , namely ,  ppbd classes ,  ppbd proteins ,  interaction search ,  tutorial and  glossary.
the  ppbd classes tab leads to the introduction pages of the 10 ppbd classes ( table 1 ) , where information about the lengths , structures , representative instances and the reported binding specificity for each of the 10 ppbd classes is presented .
the  ppbd proteins tab leads to the ppbd - containing proteins browsing page , where the user can select a ppbd - containing protein to view the details for the protein of interest , including the gene symbol , description , ncbi refseq and swiss - prot accessions and a graphical representation of all ppbd - mediated interactions involving this protein .
the information regarding the interactions involving each ppbd instance of the protein is then listed separately .
when the number of the known interactions involving a domain is sufficiently large ( 10 ) , the positional amino acid composition preference of the substrate sequences ( 17 amino acid long ) is also available as a weblogo image ( 18 ) . the  interaction search tab leads to the page where custom search functions can be executed .
the user has multiple search options for the ppbd  ppep interactions : by the ppbd class ; by the ppbd instance ; by the name , ncbi refseq accession or swiss - prot accession of either the ppbd protein or the substrate protein ; by the substrate peptide sequence , or by the pathway involved .
the search result is presented as a list of interactions , each with the names of the ppbd - containing protein and the substrate protein , the substrate sequence , index site , evidence type , category of the interaction and the number of records matching the interaction .
index site refers to the locus of the phosphorylated residue on a ppep substrate protein , or the locus of the central contact residue on a non - ppep substrate protein .
evidence type indicates the type of analysis conducted to support the presence of the interaction .
currently , four evidence types are defined : ( i ) structural determinations ; ( ii ) peptide library experiments ; ( iii ) mutagenesis and ( iv ) sequence analyses . by clicking the 
details link for each listed interaction , the user can view more detailed information about the interaction , including the names , ncbi refseq accessions , swiss - prot accessions of the ppbd - containing protein and the substrate protein , the sequence of the substrate protein , the evidence type and the references for the interactions reported .
the user can choose to plot all interactions or a selected set of interactions as ppbd - mediated protein  protein interaction networks .
the network graphs are rendered dynamically using the graph visualization software , graphviz ( 19 ) . in the network plot ,
each node represents one protein : ppbd - containing proteins are labeled in green , and other proteins are labeled in yellow .
each directed edge represents an interaction between a ppbd instance and substrate protein , with the index site displayed on the edge .
the user can click on a node representing a ppbd - containing protein to reach the ppbd protein information page .
tutorial tab leads to the page where the utility of the database is demonstrated in a graphical manner .
glossary tab leads to the glossary page where terms and abbreviations used in the web site are explained .
pepcyber : ppep is publicly accessible through the url http://www.pepcyber.org/ppep/and the data sets are available , free of charge , to researchers from academic and non - profit institutions .
the pepcyber : ppep database is a relational database implemented with mysql on a fedora core 2 linux system . the front - end web interface is implemented as a php project running under apache 2.0 .
ppbd instance , and the collection of similar ppbd instances with a high level of sequence homology and structural similarity a 
ppbd class. for example , the sh2 domain located close to the n - terminus of the protein , ptpn11 ( shp2 ) , is an 
ppbd class. presently , there are 10 reported human ppbd classes ( table 1 ) .
the current pepcyber : ppep release ( v.1.0 , release 31 july 2007 ) includes 7044 ppbd - mediated interactions involving 337 ppbd - containing proteins and 1123 substrate proteins .
this rich information was obtained through the curation of 2446 peer - reviewed research articles published between 1975 and 2007 .
the largest number of interactions involves the sh2 ppbd class ( 4290 interactions ) that is followed by the ww ppbd class ( 1389 interactions ) and 14 - 3 - 3 ppbd class ( 1086 interactions ) .
these interactions were classified into three categories based on whether the interaction was known to be mediated by a concerned ppbd instance , and whether the substrate peptide had been identified : if the interaction was known to be mediated by a ppbd instance and the substrate peptide had been identified , the interaction was classified as  category a ; if the interaction was known to be mediated by a ppbd instance but the substrate peptide had not been identified , the interaction is classified as  category b ; if it was not known whether the interaction was mediated by a ppbd instance ( though one of the interacting proteins was a ppbd protein ) , then the interaction was classified as  category c. among the 7044 interactions documented in the current release of pepcyber : ppep , 5376 ( 76% ) are category a interactions .
the 14 - 3 - 3 , ptb and ww ppbd classes are unique in that they are also capable of binding to non - ppep substrates in certain instances .
there are a total of 1068 non - ppep interactions , accounting for 15% of the total collection of the current pepcyber : ppep release .
the web interface of the pepcyber : ppep database can be accessed through the url http://www.pepcyber.org / ppep/. five tabs are located underneath the logo of the web site , namely , 
the  ppbd classes tab leads to the introduction pages of the 10 ppbd classes ( table 1 ) , where information about the lengths , structures , representative instances and the reported binding specificity for each of the 10 ppbd classes is presented .
the  ppbd proteins tab leads to the ppbd - containing proteins browsing page , where the user can select a ppbd - containing protein to view the details for the protein of interest , including the gene symbol , description , ncbi refseq and swiss - prot accessions and a graphical representation of all ppbd - mediated interactions involving this protein .
the information regarding the interactions involving each ppbd instance of the protein is then listed separately . when the number of the known interactions involving a domain is sufficiently large ( 10 ) , the positional amino acid composition preference of the substrate sequences ( 17 amino acid long ) is also available as a weblogo image ( 18 ) .
the  interaction search tab leads to the page where custom search functions can be executed .
the user has multiple search options for the ppbd  ppep interactions : by the ppbd class ; by the ppbd instance ; by the name , ncbi refseq accession or swiss - prot accession of either the ppbd protein or the substrate protein ; by the substrate peptide sequence , or by the pathway involved .
the search result is presented as a list of interactions , each with the names of the ppbd - containing protein and the substrate protein , the substrate sequence , index site , evidence type , category of the interaction and the number of records matching the interaction .
index site refers to the locus of the phosphorylated residue on a ppep substrate protein , or the locus of the central contact residue on a non - ppep substrate protein .
evidence type indicates the type of analysis conducted to support the presence of the interaction .
currently , four evidence types are defined : ( i ) structural determinations ; ( ii ) peptide library experiments ; ( iii ) mutagenesis and ( iv ) sequence analyses . by clicking the  details link for each listed interaction ,
the user can view more detailed information about the interaction , including the names , ncbi refseq accessions , swiss - prot accessions of the ppbd - containing protein and the substrate protein , the sequence of the substrate protein , the evidence type and the references for the interactions reported .
the user can choose to plot all interactions or a selected set of interactions as ppbd - mediated protein 
the network graphs are rendered dynamically using the graph visualization software , graphviz ( 19 ) . in the network plot ,
each node represents one protein : ppbd - containing proteins are labeled in green , and other proteins are labeled in yellow .
each directed edge represents an interaction between a ppbd instance and substrate protein , with the index site displayed on the edge .
the user can click on a node representing a ppbd - containing protein to reach the ppbd protein information page .
tutorial tab leads to the page where the utility of the database is demonstrated in a graphical manner .
glossary tab leads to the glossary page where terms and abbreviations used in the web site are explained .
pepcyber : ppep is publicly accessible through the url http://www.pepcyber.org/ppep/and the data sets are available , free of charge , to researchers from academic and non - profit institutions .
the pepcyber : ppep database is a relational database implemented with mysql on a fedora core 2 linux system . the front - end web interface is implemented as a php project running under apache 2.0 .
pepcyber : ppep is the first database specialized in documenting human ppbds , ppbd - containing proteins and ppbd - mediated protein  protein interactions .
however , the information about human ppbds and ppbd - mediated interactions is also hosted in existing general protein 
protein interaction databases such as bind ( 12 ) , hprd ( 13 ) and domino ( 14 ) , and functional motif databases such as elm ( 8) and phospho.elm ( 15 ) .
all these databases have different focuses , and as such the types of information stored vary among them ( table 2 ) . 

table 2.a comparison between pepcyber : ppep and similar databases in the type of information provided for ppbd - mediated protein 
protein interactionsdatabaseurlinstitution / companyppbd classppbd proteinppbd - mediated networkssubstrate proteinsubstrate sequencebinding patternindex siteevidencepathwaybindhttp://bind.caunleashed informaticsnoyesnoyesyesnonoyesnohprdhttp://www.hprd.org / institute of bioinformatics , bangalore , india and johns hopkins universityyesyesyesnonoyesnononodominohttp://mint.bio.uniroma2.it / domino / university of rome tor vergata , italyyesyesnoyesyesnoyesyesnoelmhttp://elm.eu.org / eukaryotic linear motif ( elm ) consortiumyesyesnoyesyesyesyesnoyesphospho.elmhttp://phospho.elm.eu.org/eukaryotic linear motif ( elm ) consortiumyesnonoyesyesnoyesnonopepcyber : ppephttp://www.pepcyber.org / ppep / university of minnesota , university of houston ,
protein interaction databases and host information about interactions of much broader scopes than pepcyber : ppep .
elm is a general functional motif database and has much broader scope of coverage than the ppbd substrates that pepcyber : pppep focuses on .
bold indicates that pepcyber : ppep is the database we are presenting , and that it is superior to other databases in comparison . a comparison between pepcyber : ppep and similar databases in the type of information provided for ppbd - mediated protein  protein interactions the comparison was made based only on ppbds and ppbd - mediated interactions .
protein interaction databases and host information about interactions of much broader scopes than pepcyber : ppep .
elm is a general functional motif database and has much broader scope of coverage than the ppbd substrates that pepcyber : pppep focuses on .
bold indicates that pepcyber : ppep is the database we are presenting , and that it is superior to other databases in comparison .
pepcyber : ppep hosts a substantially richer collection of data about ppbd - mediated interactions than any other database
. table 3 provides a quantitative comparison between pepcyber : ppep and the existing databases in the number of ppbd instances and ppbd - mediated interactions .
in addition to this advantageous depth and breadth of information , the pepcyber : ppep data collection is also of notably high quality , attributed to the meticulous data curation procedure followed and the rigorous quality control ( qc ) process carried out before the data is deposited into the mysql database .
for example , special attention was given to allow synonymous protein symbols used in the search , allowing a user to obtain consistent results , as different original studies may use different symbols to represent the same gene or protein . during data
curation , each gene / protein symbol used in the original articles was checked against three databases  ncbi genbank , swiss - prot and ncbi entrez gene to ensure that different symbols ( or synonyms ) of the same gene / protein are represented by the same entity in the data set . during qc
, the curated entries were checked against a local copy of the three public gene / protein databases .
if any inconsistency was identified , the entry was returned to the curation process for re - checking .
these procedures guarantee that only high - confidence data were deposited into the released pepcyber : ppep database .
problems with gene / protein symbols that occur from time to time in other databases were minimized . as an example of such problems , three symbols  shp2 , shp-2 and shptp2were used in different entries in phospho.elm , without indication that they are all synonyms of the same gene ptpn11 . 

table 3.a quantitative comparison between pepcyber : ppep and similar databases in the numbers of ppbd instances , ppbd - mediated interactions for all ppbd classes as well as for the four most popular ppbd classes : 14 - 3 - 3 , ptb , sh2 and wwdatabase#ppbd instances#ppbd - mediated interactions#14 - 3 - 3-mediated interactions#ptb - mediated interactions#sh2-mediated interactions#ww - mediated interactionsbind81149419824hprd5710577821domino195102023485468157elm1468200471phospho.elm472200112090pepcyber:ppep3377044108615842901389bold indicates that pepcyber : ppep is the database we are presenting , and that it is superior to other databases in comparison . a quantitative comparison between pepcyber : ppep and similar databases in the numbers of ppbd instances , ppbd - mediated interactions for all ppbd classes as well as for the four most popular ppbd classes : 14 - 3 - 3 , ptb , sh2 and ww bold indicates that pepcyber : ppep is the database we are presenting , and that it is superior to other databases in comparison .
pepcyber : ppep is intended to provide comprehensive , up - to - date , dynamic information and tools to researchers who require information on ppbd - mediated protein 
protein interactions as well as the sequence patterns and connecting maps of these interactions in the human proteome .
our continuing effort will be in the following several areas : ( i ) update and expand the content and functions of pepcyber : ppep as published studies on the ppbds and ppbd - mediated interactions continue to accumulate ; ( ii ) develop and implement novel analysis methods of proteins and peptides to mine the rich data compilation stored in pepcyber : ppep ; ( iii ) develop strategies and methods to predict substrate specificity for one or more ppbd instances within a ppbd class and ( iv ) develop necessary tools for systems biology modeling using the pepcyber : ppep data .
these developments will complement experimental efforts , lead to savings in time and cost in experiments , and accelerate our understanding of the key processes in cellular regulation mechanisms .
we envision that such an information source will have significant value for not only proteomic research , but also for discovery and development of drug candidates , drug targets and biomarkers .
pepcyber : ppep is merely the first significant component of the overall pepcyber , a valuable information source for important peptide - related biological and biomedical subject areas . the pepcyber effort will eventually result in a suite of database resources and computational tools assisting the development of peptide microarray - based proteomics profiling analysis .
future developments of pepcyber will include database resources with expanded scopes , e.g. non - ppbd - mediated protein  protein interactions , as well as non - database components such as peptide microarray design and data analysis tools .
 phosphoprotein - binding domains ( ppbds ) mediate many important cellular and molecular processes . 
 ten ppbds have been known to exist in the human proteome , namely , 14 - 3 - 3 , brct , c2 , fha , mh2 , pbd , ptb , sh2 , wd-40 and ww . 
 pepcyber : ppep is a newly constructed database specialized in documenting human ppbd - containing proteins and ppbd - mediated interactions . our motivation is to provide the research community with a rich information source emphasizing the reported , experimentally validated data for specific ppbd  ppep interactions . this information is not only useful for designing , comparing and validating the relevant experiments , but it also serves as a knowledge - base for computationally constructing systems signaling pathways and networks . 
 pepcyber : ppep is accessible through the url , http://www.pepcyber.org / ppep/. the current release of the database contains 7044 ppbd - mediated interactions involving 337 ppbd - containing proteins and 1123 substrate proteins . 
INTRODUCTION
UTILITY
Data content
Web interface
Data access
Implementation
COMPARISON WITH DATABASES RELEVANT TO PPBPS AND/OR PPEPS
FUTURE DIRECTIONS