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Web servers developed by Pralay

IPAC - Inference of Protein Assembly in Crystals
     The largest protein-protein contact areas in the crystal lattice are believed to reveal the natural protein- protein contacts in the physiological condition. But this is not necessarily true as the natural protein- protein contact areas can vary between a large fraction of the maximum contact area in the lattice, especially for multimers. This can result in large discrepancy in quaternary structure assessment, especially for weak protein complexes.
     We have developed one webserver for the Inference of Protein Assembly in Crystals using only atomic and lattice information. IPAC is an automated server that attempts to address some of the lacunae in current quaternary structure detection algorithms by combining a naïve Bayes classifier and point-group symmetry (PGS) under a Boolean framework to infer protein quaternary structure from atom and lattice information. Our method provides high all round coverage for strong, weak and very weak affinity homomeric and heteromeric complexes.


IPAC
Mitra, P. & Pal, D. Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference. Structure. 19(3):304-312, Mar 2011.

IPACdb - A repository for protein quaternary structures inferred from crystals
     Protein quaternary structure information is frequently used by the biologist. However, our IPAC web server takes significant amount of computation time. To facilitate the use of IPAC server and Protein Data Bank (PDB) like searching mechanism we have developed a database server, viz. IPACdb. The server contains pre-computed quaternary structures from IPAC web server and structural information from PDB. Thus, it provides reliable protein quaternary structure information along with other protein specific structural information.

IPAC

PROBE - A web server to dock two protein molecules
     The PROBE server can be used for Full docking or for Scoring and Ranking. In case of full docking, the inputs are two protein molecules and few parameters (mentioned under "Full docking"). The server will generate docking decoys using FTDock program module and score them after pruning and refining the structures. On the other hand, if someone wish to score his/her own decoys, then the inputs are two protein molecules and the transformation matrix outputted from docking search to regenerate the decoys. Then the decoys will be scored after refinement. In both the cases, the ranking will be done based on PROBE score.

JCC Graphical Abstract
Mitra, P. & Pal, D. Using correlated parameters for improved ranking of protein-protein docking decoys. J Comput Chem. 32(5):787-796, Apr 2011.
Mitra, P. & Pal, D. PRUNE and PROBE - two modular web services for protein-protein docking. Nucleic Acids Res. 39(Web Server Issue):W229-234, Jul 2011.

PRUNE - A web server to prune docking decoys
     A number of docking decoys are generated at the initial stage of any docking program (can be thought as generation stage). The number of such decoys may vary from few thousands to few hundred thousands based upon sampling of the orientation search. For example, FTDock module generates 27,720 docking decoys with default (12 degree) rotational sampling. For higher (6 degree) rotational sampling, this number increases to 222,480. Thus, reduction of the decoys is required either using edge scoring function or intergrated scoring function.
     PRUNE reduces the docking decoys generated during generation stage using edge scoring function. The input to the server is receptor and ligand protein molecules used for docking and the transformation matrix to regenerate the docking decoys. Currently, PRUNE supports file format of four docking search techniques viz., FTDock, ZDOCK, PatchDock and GrammX. The output of the server is the pruned transformation matix with the same file format as was uploaded. The option is also provided at the PRUNE result page to score and rank the pruned decoys using PROBE server.


compact
Mitra, P. & Pal, D. Using correlated parameters for improved ranking of protein-protein docking decoys. J Comput Chem. 32(5):787-796, Apr 2011.
Mitra, P. & Pal, D. PRUNE and PROBE - two modular web services for protein-protein docking. Nucleic Acids Res. 39(Web Server Issue):W229-234, Jul 2011.

dockYard - A repository of protein-protein docking decoys
     The dockYard is a repository of protein-protein docking decoys. The main purpose of dockYard is to aid researchers involved in developing scoring function for protein-protein docking, by actually providing them with a large set of docking decoys. The intention is to significantly reduce the burden of computation, otherwise required to generate these decoys first hand in silico. dockYard supplies initial coordinates and transformation matrices using which user can generate all the docking decoys in his/her system locally without implementing/installing docking search algorithms. The search page of dockYard helps to screen for docking decoys using various parameters, including UniRef and SCOP.

dockYard Scheme
Mitra, P. & Pal, D. dockYard - a repository to assist modeling of protein-protein docking. J Mol Model. 17(3):599-606, Mar 2011.

COMPACT - A naive Bayse classifier for identifying biological interfaces
COMplementarity and PACking at inTerfaces (COMPACT) is a web server to find biological interfacses from crystal lattice if any present. If you upload a protein complex in PDB format with crystallopgraphic information then the server will generate the crystal lattice and will compute ten features at the subunit contacts. The naive Bayse classifier will then be employed to classify the contacts as biological or not. The classifier is trained by a set of known dimeric and monomeric protein interfaces. The server is useful for discriminating dimeric and monomeric proteins. To know the quaternary state (multimer) please use IPAC server.

compact
Mitra, P. & Pal, D. Combining Bayes classification and point group symmetry under Boolean framework for enhanced protein quaternary structure inference. Structure. 19(3):304-312, Mar 2011.

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Last modified: Aug, 2011.