title: HotRegion: a database of predicted hot spot clusters.
abstract: Hot spots are energetically important residues at protein interfaces and they are not randomly distributed across the interface but rather clustered. These clustered hot spots form hot regions. Hot regions are important for the stability of protein complexes, as well as providing specificity to binding sites. We propose a database called HotRegion, which provides the hot region information of the interfaces by using predicted hot spot residues, and structural properties of these interface residues such as pair potentials of interface residues, accessible surface area (ASA) and relative ASA values of interface residues of both monomer and complex forms of proteins. Also, the 3D visualization of the interface and interactions among hot spot residues are provided. HotRegion is accessible at http://prism.ccbb.ku.edu.tr/hotregion.
authors.affiliation: Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey.
authors.forename: Engin
authors.initials: E
authors.lastname: Cukuroglu
authors.forename: Attila
authors.initials: A
authors.lastname: Gursoy
authors.forename: Ozlem
authors.initials: O
authors.lastname: Keskin
mesh_terms: D001665:Binding Sites; D016000:Cluster Analysis; D030562:Databases, Protein; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D046912:Multiprotein Complexes
references.citation: Proc Natl Acad Sci U S A. 2006 Jun 27;103(26):9867-72
references.pmid: 16788072
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4347-52
references.pmid: 17360527
references.citation: Genome Biol. 2007;8(5):R92
references.pmid: 17531094
references.citation: Bioinformatics. 2009 Jun 15;25(12):1513-20
references.pmid: 19357097
references.citation: PLoS Comput Biol. 2007 Aug;3(8):e164
references.pmid: 17722975
references.citation: J Mol Biol. 2005 Feb 4;345(5):1281-94
references.pmid: 15644221
references.citation: J Mol Biol. 2001 Mar 16;307(1):447-63
references.pmid: 11243830
references.citation: Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15447-52
references.pmid: 16221766
references.citation: Proteomics. 2009 Apr;9(7):1744-53
references.pmid: 19253304
references.citation: Proc Natl Acad Sci U S A. 2002 Oct 29;99(22):14116-21
references.pmid: 12381794
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W402-6
references.pmid: 20444871
references.citation: Methods Enzymol. 1991;202:390-411
references.pmid: 1723781
references.citation: PLoS Comput Biol. 2010 Jun 17;6(6):e1000821
references.pmid: 20585553
references.citation: J Mol Biol. 2008 Sep 5;381(3):785-802
references.pmid: 18620705
references.citation: Science. 2006 Dec 22;314(5807):1938-41
references.pmid: 17185604
references.citation: Proteins. 2011 Sep;79(9):2671-83
references.pmid: 21735484
references.citation: Proc Natl Acad Sci U S A. 2005 Jan 4;102(1):57-62
references.pmid: 15618400
references.citation: J Comput Aided Mol Des. 2009 Sep;23(9):645-54
references.pmid: 19479323
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Structure. 2004 Jun;12(6):1027-38
references.pmid: 15274922
references.citation: Biochem Mol Biol Educ. 2006 Jul;34(4):255-61
references.pmid: 21638687
references.citation: Proc Natl Acad Sci U S A. 2010 Jun 1;107(22):10080-5
references.pmid: 20479265
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D662-6
references.pmid: 17959648
references.citation: BMC Biol. 2007 Oct 09;5:43
references.pmid: 17925020
references.citation: Trends Biochem Sci. 2001 Oct;26(10):624-31
references.pmid: 11590016
references.citation: Protein Sci. 2009 Aug;18(8):1674-83
references.pmid: 19591200
references.citation: Proteins. 2002 May 15;47(3):334-43
references.pmid: 11948787
references.citation: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W398-401
references.pmid: 20457748
references.citation: Structure. 2007 Mar;15(3):341-54
references.pmid: 17355869
references.citation: J Mol Biol. 1996 Jul 26;260(4):604-20
references.pmid: 8759323
references.citation: J Comput Chem. 2010 Nov 30;31(15):2677-88
references.pmid: 20839295
references.citation: Ann Biomed Eng. 2010 Jun;38(6):2068-78
references.pmid: 20437205
references.citation: Science. 1995 Jan 20;267(5196):383-6
references.pmid: 7529940
references.citation: Phys Biol. 2005 Jun;2(2):S24-35
references.pmid: 16204846
references.citation: Protein Sci. 2004 Apr;13(4):1043-55
references.pmid: 15044734
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W260-4
references.pmid: 18467424
references.citation: J Mol Biol. 1998 Jul 3;280(1):1-9
references.pmid: 9653027