Predicting active site residue annotations in the Pfam database

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Mistry, Jaina ^a   Bateman, Alex ^a   Finn, Robert D ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ACTIVE SITE RESIDUES; CATALYTIC SITES; FALSE POSITIVE; LARGE DATABASE; SENSITIVITY AND SPECIFICITY; SET OF RULES;

FORECASTING;

DATABASE SYSTEMS;

AMINO ACID SEQUENCE; ARTICLE; ENZYME ACTIVE SITE; FALSE POSITIVE RESULT; INFORMATION PROCESSING; INTERMETHOD COMPARISON; METHODOLOGY; NUCLEOTIDE SEQUENCE; PFAM DATABASE; PREDICTION; PROTEIN DATABASE; PROTEIN DOMAIN; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; BINDING SITE; COMPARATIVE STUDY; COMPUTER PROGRAM; MOLECULAR GENETICS; PREDICTION AND FORECASTING; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BINDING SITES; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; PREDICTIVE VALUE OF TESTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE DESIGN;

EID: 35348873256     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-298     Document Type: Article

References (32)

1. Finn RD Mistry J Schuster-Bockler B Griffiths-Jones S Hollich V Lassmann T Moxon S Marshall M Khanna A Durbin R Eddy SR Sonnhammer EL Bateman A Pfam: Clans, web tools and services Nucleic Acids Res 2006, 34(Database issue):D247-51. 1347511 16381856 10.1093/nar/gkj149
2. Ben-Shimon A Eisenstein M Looking at enzymes from the inside out: The proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces J Mol Biol 2005, 351(2):309-326. 10.1016/j.jmb.2005.06.047 16019028
3. Chou KC Cai YD A novel approach to predict active sites of enzyme molecules Proteins 2004, 55(1):77-82. 10.1002/prot.10622 14997541
4. Ota M Kinoshita K Nishikawa K Prediction of catalytic residues in enzymes based on known tertiary structure, stability profile, and sequence conservation J Mol Biol 2003, 327(5):1053-1064. 10.1016/ S0022-2836(03)00207-9 12662930
5. Greaves R Warwicker J Active site identification through geometry-based and sequence profile-based calculations: Burial of catalytic clefts J Mol Biol 2005, 349(3):547-557. 10.1016/j.jmb.2005.04.018 15882869
6. Elcock AH Prediction of functionally important residues based solely on the computed energetics of protein structure J Mol Biol 2001, 312(4):885-896. 10.1006/jmbi.2001.5009 11575940
7. Beadle BM Shoichet BK Structural bases of stability-function tradeoffs in enzymes J Mol Biol 2002, 321(2):285-296. 10.1016/ S0022-2836(02)00599-5 12144785
8. Zvelebil MJ Sternberg MJ Analysis and prediction of the location of catalytic residues in enzymes Protein Eng 1988, 2(2):127-138. 10.1093/ protein/2.2.127 3244695
9. Mayer KM McCorkle SR Shanklin J Linking enzyme sequence to function using Conserved Property Difference Locator to identify and annotate positions likely to control specific functionality BMC Bioinformatics 2005, 6:284. 1326233 16318626 10.1186/1471-2105-6-284
10. Tian W Arakaki AK Skolnick J EFICAz: A comprehensive approach for accurate genome-scale enzyme function inference Nucleic Acids Res 2004, 32(21):6226-6239. 535665 15576349 10.1093/nar/gkh956
11. Panchenko AR Kondrashov F Bryant S Prediction of functional sites by analysis of sequence and structure conservation Protein Sci 2004, 13(4):884-892. 10.1110/ps.03465504 15010543
12. Lichtarge O Bourne HR Cohen FE An evolutionary trace method defines binding surfaces common to protein families J Mol Biol 1996, 257(2):342-358. 10.1006/jmbi.1996.0167 8609628
13. Yao H Kristensen DM Mihalek I Sowa ME Shaw C Kimmel M Kavraki L Lichtarge O An accurate, sensitive, and scalable method to identify functional sites in protein structures J Mol Biol 2003, 326(1):255-261. 10.1016/S0022-2836(02)01336-0 12547207
14. Yao H Mihalek I Lichtarge O Rank information: A structure-independent measure of evolutionary trace quality that improves identification of protein functional sites Proteins 2006, 65(1):111-123. 10.1002/ prot.21101 16894615
15. Aloy P Querol E Aviles FX Sternberg MJ Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking J Mol Biol 2001, 311(2):395-408. 10.1006/jmbi.2001.4870 11478868
16. La D Livesay DR Predicting functional sites with an automated algorithm suitable for heterogeneous datasets BMC Bioinformatics 2005, 6:116. 1142304 15890082 10.1186/1471-2105-6-116
17. Liu AH Zhang X Stolovitzky GA Califano A Firestein SJ Motif-based construction of a functional map for mammalian olfactory receptors Genomics 2003, 81(5):443-456. 10.1016/S0888-7543(03)00022-3 12706103
18. Puntervoll P Linding R Gemund C Chabanis-Davidson S Mattingsdal M Cameron S Martin DM Ausiello G Brannetti B Costantini A Ferre F Maselli V Via A Cesareni G Diella F Superti-Furga G Wyrwicz L Ramu C McGuigan C Gudavalli R Letunic I Bork P Rychlewski L Kuster B Helmer-Citterich M Hunter WN Aasland R Gibson TJ ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins Nucleic Acids Res 2003, 31(13):3625-3630. 168952 12824381 10.1093/nar/ gkg545
19. Gutteridge A Bartlett GJ Thornton JM Using a neural network and spatial clustering to predict the location of active sites in enzymes J Mol Biol 2003, 330(4):719-734. 10.1016/S0022-2836(03)00515-1 12850142
20. Dobson PD Doig AJ Distinguishing enzyme structures from non-enzymes without alignments J Mol Biol 2003, 330(4):771-783. 10.1016/ S0022-2836(03)00628-4 12850146
21. Petrova NV Wu CH Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties BMC Bioinformatics 2006, 7:312. 1534064 16790052 10.1186/1471-2105-7-312
22. Porter CT Bartlett GJ Thornton JM The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res 2004, 32(Database issue):D129-33. 308762 14681376 10.1093/nar/gkh028
23. Wu CH Apweiler R Bairoch A Natale DA Barker WC Boeckmann B Ferro S Gasteiger E Huang H Lopez R Magrane M Martin MJ Mazumder R O'Donovan C Redaschi N Suzek B The Universal Protein Resource (UniProt): An expanding universe of protein information Nucleic Acids Res 2006, 34(Database issue):D187-91. 1347523 16381842 10.1093/nar/gkj161
24. Hulo N Bairoch A Bulliard V Cerutti L De Castro E Langendijk-Genevaux PS Pagni M Sigrist CJ The PROSITE database Nucleic Acids Res 2006 34 Database issue 2006, 34(Database issue):D227-30. 1347426 16381852 10.1093/nar/gkj063
25. Mulder NJ Apweiler R Attwood TK Bairoch A Bateman A Binns D Bork P Buillard V Cerutti L Copley R Courcelle E Das U Daugherty L Dibley M Finn R Fleischmann W Gough J Haft D Hulo N Hunter S Kahn D Kanapin A Kejariwal A Labarga A Langendijk-Genevaux PS Lonsdale D Lopez R Letunic I Madera M Maslen J McAnulla C McDowall J Mistry J Mitchell A Nikolskaya AN Orchard S Orengo C Petryszak R Selengut JD Sigrist CJ Thomas PD Valentin F Wilson D Wu CH Yeats C New developments in the InterPro database Nucleic Acids Res 2007, 35(Database issue):D224-8. 1899100 17202162 10.1093/nar/gkl841
26. Nevill-Manning CG Wu TD Brutlag DL Highly specific protein sequence motifs for genome analysis Proc Natl Acad Sci U S A 1998, 95(11):5865-5871. 34488 9600885 10.1073/pnas.95.11.5865
27. Letunic I Copley RR Pils B Pinkert S Schultz J Bork P SMART 5: Domains in the context of genomes and networks Nucleic Acids Res 2006 34 Database issue 2006, 34(Database issue):D257-60. 16381859 10.1093/nar/ gkj079
28. Rawlings ND Morton FR Barrett AJ MEROPS: The peptidase database Nucleic Acids Res 2006, 34(Database issue):D270-2. 1347452 16381862 10.1093/nar/ gkj089
29. Velankar S McNeil P Mittard-Runte V Suarez A Barrell D Apweiler R Henrick K E-MSD: An integrated data resource for bioinformatics Nucleic Acids Res 2005, 33(Database issue):D262-5. 540012 15608192 10.1093/nar/ gki058
30. Sonnhammer EL Eddy SR Durbin R Pfam: A comprehensive database of protein domain families based on seed alignments Proteins 1997, 28(3):405-420. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L 9223186
31. Finn RD Stalker JW Jackson DK Kulesha E Clements J Pettett R ProServer: A simple, extensible Perl DAS server Bioinformatics 2007.
32. Eddy SR Profile hidden Markov models Bioinformatics 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755 9918945