increasing structural genomics projects have led to the exponential growth of the number of available protein structures . a few of these structures are annotated as hypothetical proteins as biochemical information is not available for them
the importance of such a tool is strengthened by the automation required for structural genomics projects .
a large number of theoretical tools exist that attempt to predict functions of proteins on the basis of sequence or structural homology of the query protein with well - characterized proteins .
however , proteins having sequence or structural similarity might not always perform similar biological functions ( 1,2 ) .
proteins possessing different folds are also known to perform similar functions such as subtilisin - like proteases and trypsin - like proteases ( 3 ) .
this discrepancy has led to the development of structure - based approaches wherein function is predicted on the basis of similarity of the spatial arrangement of functionally significant residues .
structure - based approaches ( 39 ) typically attempt to identify residues that might be non - contiguous in the primary sequence but are structurally analogous with a known structural template .
such approaches are guided by the fact that proteins perform similar function by maintaining the physicochemical environment of their functionally significant residues .
this fact can be exploited to generate structural templates from active site geometries of known enzymes , and then comparing the newly determined structures with these templates .
methods that create structural templates from c atoms of the active site residues and their spatial neighbors have a drawback of lacking specificity and thereby giving rise to a large number of false positives .
the other methods that use all the side - chain atoms of the key residues are too constrained and often overlook the small variations that might occur in the side chain placements . in our method , we use c atoms of the key residues along with the corresponding c atoms to form a template . these templates possess optimum specificity and flexibility to identify active site residues in query structures .
the method is not affected by the small conformational variations and ambiguities in the placement of side - chains in the query structure .
in addition to this the algorithm employed does not require any similarity to overall sequence or fold of known proteins . in this article
we describe a web - server that executes this structure - based approach for predicting function .
the method of iengar and ramakrishnan ( 10 ) has been modified and implemented in the current server .
structural templates are generated for the active site residues of different protease classes , glycolytic pathway enzymes and metal - binding sites .
a training set was formulated from a set of known proteins of each functional family .
the structural templates consist of active site residues identity and the geometrical parameters derived from their spatial environment .
the geometrical parameters considered are the distances between the c and c atoms of the active site residues and the angle between the c plane and the c plane .
the c and c planes are defined by the c or c atoms , respectively of the residues comprising the active site ( figure 2a ) .
geometrical parameters for all the structural motifs are calculated and stored for the prediction ( http://sunserver.cdfd.org.in:8080/protease/par_3d/motif.html ) .
merops database ( 11,12 ) was used to form training sets for different protease classes .
the clan identifiers along with the active site residue pattern are shown ( figure 1 ) .
templates could not be generated for other clans either due to non - availability of sufficient representative structures or due to involvement of less than three residues in the catalytic activity . 

structural templates represent six clans described in the merops database . the clan identifier and the primary sequence order of their active site residues
structural templates represent six clans described in the merops database . the clan identifier and the primary sequence order of their active site residues
the algorithm employed here performs well for all the structures solved by x - ray crystallography , nmr spectroscopy and theoretical structure prediction tools . in the case of nmr structures
however , the server is especially useful for structures modeled by threading , because inaccurate side chain placement in the threading - based models does not affect the accuracy of active - site residue prediction .
a two - step procedure is used to identify active site residues for every query structure . in the first step coordinates of residues that can form the active site
are extracted from the query structure file . in the second step spatial arrangement of the probable active site residues
the user is required to provide a single query structure file in a pdb format .
the user submitted structure files are accepted through an html form generated using cgi - perl script . in order to search for a rcsb file , it has to be downloaded on a local machine and then submitted to par-3d .
par-3d stores structural motifs for different protease classes , glycolytic pathway enzymes and metal - binding sites .
the user can specify if they wish to search against one family of motifs or all the par-3d motifs . the uploaded file is first tested and verified for the pdb format .
the structure data obtained are then processed by a set of perl scripts that search for the stored structural templates .
output is provided in a tabular format describing the list of predicted active site residues .
a sample output produced using yeast ydr533c structure ( pdb i d : 1qvv ) is shown in figure 2b .
the structural motifs stored here for the comparison are specific for different protease classes , glycolytic pathway enzymes and metal - binding sites .
therefore , output also provides information about the functional class of the predicted site in the query structure . 

the seven parameters used to define the template are distances between three c atoms , distances between three c atoms and the angle between the planes formed by the three c and the three c atoms of the active site residues .
( b ) output of a search carried out for yeast ydr533c structure ( 1qvv ) shows a putative metal - binding site predicted by par-3d .
the seven parameters used to define the template are distances between three c atoms , distances between three c atoms and the angle between the planes formed by the three c and the three c atoms of the active site residues .
( b ) output of a search carried out for yeast ydr533c structure ( 1qvv ) shows a putative metal - binding site predicted by par-3d .
algorithm implemented here predicts the functional class of the query structure on the basis of the spatial arrangement and the residue identity of the predicted catalytic residues .
however , it is known that several functional classes belonging to the superfamily hydrolases , such as acetyl - choline esterases , acetonitriles , lipases , serine carboxypeptidases , all possess similar catalytic triads as serine carboxypeptidases due to similar catalytic mechanism .
therefore , a query structure from any of these hydrolases will be predicted as serine carboxypeptidases .
the server ( par-3d ) has been tested extensively and response time has been observed to be 12  min .
the local running time of the same was 0.3 cpu seconds on a silicon graphics workstation with r10000 processor .
the statistics of par-3d performance upon scanning the complete pdb can be accessed at http://sunserver.cdfd.org.in:8080/protease/par_3d/statistics.html .
presently the server searches for structural motifs derived from proteases , glycolytic pathway enzymes and metal - binding sites .
we are currently working to generate structural motifs for other functionally important sites in proteins .
we are also working to include a feature , which will help to engineer new catalytic sites in existing proteins . with the availability of structural motif for several functional classes of proteins ,
 par-3d ( http://sunserver.cdfd.org.in:8080/protease/par_3d/index.html ) is a web - based tool that exploits the fact that relative juxtaposition of active site residues is a conserved feature in functionally related protein families . the server uses previously calculated and stored values of geometrical parameters of a set of known proteins ( training set ) for prediction of active site residues in a query protein structure . 
 par-3d stores motifs for different classes of proteases , the ten glycolytic pathway enzymes and metal - binding sites . 
 the server accepts the structures in the pdb format . 
 the first step during the prediction is the extraction of probable active site residues from the query structure . 
 spatial arrangement of the probable active site residues is then determined in terms of geometrical parameters . 
 these are compared with stored geometries of the different motifs . 
 its speed and efficiency make it a beneficial tool for structural genomics projects , especially when the biochemical function of the protein has not been characterized . 
INTRODUCTION
IMPLEMENTATION
INPUT AND OUTPUT
LIMITATION
PERFORMANCE AND AVAILABILITY
CONCLUSION AND FUTURE WORK