title: Binding ligand prediction for proteins using partial matching of local surface patches.
abstract: Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group.
authors: Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; E-Mail: lee399@cs.purdue.edu.
authors: Lee
authors: L
authors: Sael
authors: Daisuke
authors: D
authors: Kihara
references: Curr Opin Struct Biol. 2005 Jun;15(3):267-74
references: 15922590
references: Bioinformatics. 2009 Nov 1;25(21):2843-4
references: 19759195
references: J Mol Biol. 2006 Feb 3;355(5):1112-24
references: 16359705
references: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references: 10592235
references: J Struct Biol. 2008 Jan;161(1):31-42
references: 17949996
references: Proteins. 2004 May 1;55(2):464-73
references: 15048836
references: J Mol Biol. 2001 Sep 28;312(4):885-96
references: 11575940
references: Curr Protein Pept Sci. 2011 Sep;12(6):520-30
references: 21787306
references: J Mol Graph. 1992 Dec;10(4):229-34
references: 1476996
references: Science. 2006 Jan 20;311(5759):347-51
references: 16424331
references: Proteins. 2008 Oct;73(1):1-10
references: 18618695
references: Cell Biochem Biophys. 2009;54(1-3):23-32
references: 19521674
references: J Mol Biol. 2007 Apr 20;368(1):283-301
references: 17337005
references: Proteins. 2010 Jul;78(9):2007-28
references: 20455259
references: Proteins. 2008 May 1;71(2):670-83
references: 17975834
references: BMC Bioinformatics. 2010 Feb 22;11:99
references: 20175916
references: Annu Rev Biochem. 2005;74:867-900
references: 15954844
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W398-402
references: 17567616
references: BMC Bioinformatics. 2010 Dec 14;11 Suppl 11:S2
references: 21172052
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D129-33
references: 14681376
references: BMC Bioinformatics. 2009 Dec 09;10:407
references: 20003235
references: J Mol Biol. 2009 Mar 27;387(2):451-64
references: 19154742
references: Curr Opin Struct Biol. 2005 Jun;15(3):275-84
references: 15963890
references: Bioinformatics. 2005 May 1;21(9):1908-16
references: 15701681
references: J Mol Graph. 1995 Oct;13(5):323-30, 307-8
references: 8603061
references: Mol Cell Proteomics. 2005 Jun;4(6):752-61
references: 15757999
references: Chem Cent J. 2007 Mar 13;1:7
references: 17880740
references: BMC Bioinformatics. 2007 Mar 08;8 Suppl 1:S24
references: 17430569
references: Structure. 2005 Jan;13(1):121-30
references: 15642267
references: Brief Bioinform. 2009 Jul;10(4):378-91
references: 19324930
references: Nature. 1994 Dec 15;372(6507):631-4
references: 7990952
references: Bioinformatics. 2005 May 15;21(10):2347-55
references: 15728116
references: J Cheminform. 2009 Dec 17;1:19
references: 20150998
references: Proteins. 2008 Sep;72(4):1259-73
references: 18361455
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D240-4
references: 14681403
references: Bioinformatics. 2004 May 1;20(7):1087-96
references: 14764543
references: Mol Biosyst. 2008 Mar;4(3):223-31
references: 18437265
references: BMC Struct Biol. 2006 Sep 24;6:19
references: 16995956
references: Protein Sci. 1998 Sep;7(9):1884-97
references: 9761470
references: J Bioinform Comput Biol. 2007 Feb;5(1):1-30
references: 17477489
references: Proteins. 2007 Aug 1;68(2):516-29
references: 17444522