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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