Web Servers

Database Servers

Software

As part of our research work, we implemented and tested all of our algorithms. Those implementations are made available as free web services for the research community. The predicted data of our method is made available through free database servers. Some of the implemetations are also available as binary code. The front-end of the servers are implemented in PHP and HTML, whereas, the back-end methods are implemented using C, C++, Fortran, Python and PERL.

Web Servers

  • EvoDesign - de novo protein design webserver

         Mitra, P., Shultis, D. & Zhang, Y. (2013) Nucleic Acids Res. 41, In press.
         EvoDesign is an evolutionary profile based approach to de novo protein design. Starting from a scaffold of target protein structure, EvoDesign first identifies protein families which have similar fold from the PDB library by TM-align. A structural profile is then constructed from the protein templates which is used to guide the conformation search of amino acid sequence space, where physicochemical packing is accommodated by the single-sequence based solvation, torsion angle and secondary structure predictions. The final designed sequence is obtained by clustering all sequence decoys generated during design simulations.
  • IPAC
  • IPAC - Inference of Protein Assembly in Crystals

         Mitra, P. & Pal, D. (2011) Structure 19, 304-312.
         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 automated webserver by combining a naive 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
  • PROBE - A web server to dock two protein molecules

         Mitra, P. & Pal, D. (2011) J Comput Chem. 32, 787-796.
         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
  • PRUNE - A web server to prune docking decoys    Omics-tools

         Mitra, P. & Pal, D. (2011) Nucleic Acids Res. 39, W229-234.
         A number of docking decoys are generated at the initial stage of any docking program. The number of such decoys may vary from thousands to several hundred thousands based upon sampling density. 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 formats of FTDock, ZDOCK, PatchDock and GrammX docking search techniques. The output of the server is the pruned transformation matix with the same file format as was uploaded. The option is provided at the PRUNE result page to score and rank the pruned decoys using PROBE server.
  • compact

    Database Servers

  • IPACdb - A repository for protein quaternary structures inferred from crystals

         Mitra, P. & Pal, D. (2011) Structure 19, 304-312.
         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
  • dockYard - A repository of protein-protein docking decoys

         Mitra, P. & Pal, D. (2011) J Mol Model. 17, 599-606.
         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

    Softwares

    • NIP-NSc - Normalized Interface Packing & Normalized Surface Complementarity