title: HotPoint: hot spot prediction server for protein interfaces.
abstract: The energy distribution along the protein-protein interface is not homogenous; certain residues contribute more to the binding free energy, called 'hot spots'. Here, we present a web server, HotPoint, which predicts hot spots in protein interfaces using an empirical model. The empirical model incorporates a few simple rules consisting of occlusion from solvent and total knowledge-based pair potentials of residues. The prediction model is computationally efficient and achieves high accuracy of 70%. The input to the HotPoint server is a protein complex and two chain identifiers that form an interface. The server provides the hot spot prediction results, a table of residue properties and an interactive 3D visualization of the complex with hot spots highlighted. Results are also downloadable as text files. This web server can be used for analysis of any protein-protein interface which can be utilized by researchers working on binding sites characterization and rational design of small molecules for protein interactions. HotPoint is accessible at http://prism.ccbb.ku.edu.tr/hotpoint.
authors.affiliation: Center for Computational Biology and Bioinformatics, and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
authors.forename: Nurcan
authors.initials: N
authors.lastname: Tuncbag
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
authors.forename: Attila
authors.initials: A
authors.lastname: Gursoy
mesh_terms: D001665:Binding Sites; D007376:Interleukin-2 / Q000737:chemistry; D020407:Internet; D046912:Multiprotein Complexes / Q000737:chemistry*; D025941:Protein Interaction Mapping / Q000379:methods*; D015375:Receptors, Interleukin-2 / Q000737:chemistry; D012984:Software; D014584:User-Computer Interface
chemical_list: D007376:Interleukin-2; D046912:Multiprotein Complexes; D015375:Receptors, Interleukin-2
references.citation: PLoS Comput Biol. 2007 Jul;3(7):e119
references.pmid: 17630824
references.citation: Proc Natl Acad Sci U S A. 2004 Aug 3;101(31):11287-92
references.pmid: 15269345
references.citation: J Comput Aided Mol Des. 2009 Sep;23(9):645-54
references.pmid: 19479323
references.citation: Bioinformatics. 2009 Jun 15;25(12):1513-20
references.pmid: 19357097
references.citation: Nucleic Acids Res. 2009 May;37(8):2672-87
references.pmid: 19273533
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6
references.pmid: 17959648
references.citation: Sci STKE. 2004 Feb 03;2004(219):pl2
references.pmid: 14872095
references.citation: Curr Med Chem. 2006;13(22):2607-25
references.pmid: 17017914
references.citation: Proteins. 2007 Sep 1;68(4):813-23
references.pmid: 17554779
references.citation: Nucleic Acids Res. 2010 Apr;38(6):e86
references.pmid: 20008102
references.citation: Science. 1995 Jan 20;267(5196):383-6
references.pmid: 7529940
references.citation: Proc Natl Acad Sci U S A. 2006 Oct 17;103(42):15422-7
references.pmid: 17032757
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W265-9
references.pmid: 18539611
references.citation: Methods Enzymol. 1991;202:390-411
references.pmid: 1723781
references.citation: Protein Sci. 1998 Dec;7(12):2578-86
references.pmid: 9865952
references.citation: Biochem Mol Biol Educ. 2006 Jul;34(4):255-61
references.pmid: 21638687
references.citation: Curr Pharm Biotechnol. 2008 Apr;9(2):67-76
references.pmid: 18393863
references.citation: Bioinformatics. 2001 Mar;17(3):284-5
references.pmid: 11294795
references.citation: BMC Bioinformatics. 2009 Oct 30;10:365
references.pmid: 19878545
references.citation: J Mol Biol. 2005 Feb 4;345(5):1281-94
references.pmid: 15644221
references.citation: J Mol Biol. 2002 Jul 5;320(2):369-87
references.pmid: 12079393
references.citation: J Comput Chem. 2002 Jan 15;23(1):15-27
references.pmid: 11913381
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14116-21
references.pmid: 12381794
references.citation: Chem Rev. 2008 Apr;108(4):1225-44
references.pmid: 18355092
references.citation: J Mol Biol. 1998 Jul 3;280(1):1-9
references.pmid: 9653027
references.citation: Bioinformatics. 2003 Jul 22;19(11):1453-4
references.pmid: 12874065