Acknowledgement
We are greateful to researchers for their help in developing this database. We are thankful to Dr Roman Laskowski, European Bioinformatics Institute, UK for his help. In this database we used information from various resources/database as well as we used number of software/web services for developing this database. We are grateful to the developers of these databases/software/resopurces that include following resources.
| PROMOTIF--a program to identify and analyze structural motifs in proteins. |
| Hutchinson EG, Thornton JM. PROMOTIF--a program to identify and analyze structural motifs in proteins. Protein Sci. 1996 Feb;5(2):212-20.PMID:8745398 |
| The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. |
| Hooft RW, Sander C, Scharf M, Vriend G. The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value. Comput Appl Biosci. 1996 Dec;12(6):525-9. PMID:9021272 |
| The RCSB Protein Data Bank: redesigned web site and web services. |
| Rose PW, Beran B, Bi C, Bluhm WF, Dimitropoulos D, Goodsell DS, Prlic A, Quesada M, Quinn GB, Westbrook JD, Young J, Yukich B, Zardecki C, Berman HM, Bourne PE. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 2011 Jan;39(Database issue):D392-401. PMID:21036868 |
| HMMER3: a new generation of sequence homology search software |
| Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009 Oct;23(1):205-11. PMID:20180275 |
| The Pfam protein families database |
| R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, J.E. Pollington, O.L. Gavin, P. Gunesekaran, G. Ceric, K. Forslund, L. Holm, E.L. Sonnhammer, S.R. Eddy, A. Bateman Nucleic Acids Research (2010) Database Issue 38:D211-222. PMID:19920124 |
| DSSP: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features |
| Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577-637. PMID:6667333 |
| fpocket:An open source platform for ligand pocket detection |
| Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery, "Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics, 2009, 10:168 PMID:19486540 |
| LPC : Ligand-Protein Contacts |
| Ligand-Protein Contacts (LPC) were derived with LPC software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). PMID:10320401 |
| Protein-DNA Interface Database (PDIDB) |
| Norambuena T, Melo F. The Protein-DNA Interface database. BMC Bioinformatics. 2010 May 18;11:262. PMID:20482798 |