Tools for comparative protein structure modeling and analysis

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3375-3380

  Eswar, Narayanan ^d   John, Bino ^a   Mirkovic, Nebojsa ^a   Fiser, Andras ^b   Ilyin, Valentin A ^c   Pieper, Ursula ^d   Stuart, Ashley C ^a   Marti Renom, Marc A ^d   Madhusudhan, M S ^d   Yerkovich, Bozidar ^a   Sali, Andrej ^d  

^a ROCKEFELLER UNIVERSITY   (United States)

^b ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^c NORTHEASTERN UNIVERSITY   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

AMINO ACID SUBSTITUTION; ANALYTIC METHOD; ARTICLE; AUTOMATION; COMPARATIVE STUDY; COMPUTER ANALYSIS; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER PROGRAM; COMPUTER SYSTEM; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; INTERNET; PROTEIN FOLDING; REPRODUCIBILITY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; SYSTEM ANALYSIS;

INTERNET; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEINS; REPRODUCIBILITY OF RESULTS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN; SYSTEMS INTEGRATION;

EID: 0043123167     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg543     Document Type: Article

References (38)

1. Zhang,C. and Kim,S.H. (2003) Overview of structural genomics: from structure to function. Curr. Opin. Chem. Biol., 7, 28-32.
2. Boeckmann,B., Bairoch,A., Apweiler,R., Blatter,M.C., Estreicher,A., Gasteiger,E., Martin,M.J., Michoud,K., O'Donovan,C., Phan,I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
3. Berman,H.M., Battistuz,T., Bhat,T.N., Bluhm,W.F., Bourne,P.E., Burkhardt,K., Feng,Z., Gilliland,G.L., Iype,L., Jain,S. et al. (2002) The Protein Data Bank. Acta Crystallogr. D. Biol. Crystallogr., 58, 899-907.
4. Vitkup,D., Melamud,E., Moult,J. and Sander,C. (2001) Completeness in structural genomics. Nature Struct. Biol., 8, 559-566.
5. Domingues,F.S., Lackner,P., Andreeva,A. and Sippl,M.J. (2000) Structure-based evaluation of sequence comparison and fold recognition alignment accuracy. J. Mol. Biol., 297, 1003-1013.
6. Blundell,T.L., Sibanda,B.L., Sternberg,M.J. and Thornton,J.M. (1987) Knowledge-based prediction of protein structures and the design of novel molecules. Nature, 326, 347-352.
7. Marti-Renom,M.A., Stuart,A.C., Fiser,A., Sanchez,R., Melo,F. and Sali,A. (2000) Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct., 29, 291-325.
8. Sali,A. (1998) 100,000 protein structures for the biologist. Nature Struct. Biol., 5, 1029-1032.
9. Sanchez,R., Pieper,U., Melo,F., Eswar,N., Marti-Renom,M.A., Madhusudhan,M.S., Mirkovic,N. and Sali,A. (2000) Protein structure modeling for structural genomics. Nature Struct. Biol., 7 (suppl.), 986-990.
10. Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
11. Chothia,C. and Lesk,A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
12. Sanchez,R. and Sali,A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl Acad. Sci. USA, 95, 13597-13602.
13. Fischer,D., Elofsson,A., Rychlewski,L., Pazos,F., Valencia,A., Rost,B., Ortiz,A.R. and Dunbrack,R.L., Jr. (2001) CAFASP2: the second critical assessment of fully automated structure prediction methods. Proteins, 5 (suppl.), 171-183.
14. Bujnicki,J.M., Elofsson,A., Fischer,D. and Rychlewski,L. (2001) LiveBench-2: large-scale automated evaluation of protein structure prediction servers. Proteins, 5 (suppl.), 184-191.
15. Koh,I.Y.Y., Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Eswar,N., Graña,O., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2003) EVA: evaluation of protein structure prediction servers. Nucleic Acids Res., 31, 3311-3315.
16. Eyrich,V.A., Marti-Renom,M.A., Przybylski,D., Madhusudhan,M.S., Fiser,A., Pazos,F., Valencia,A., Sali,A. and Rost,B. (2001) EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics, 17, 1242-1243.
17. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
18. Fiser,A., Do,R.K. and Sali,A. (2000) Modeling of loops in protein structures. Protein Sci., 9, 1753-1773.
19. MacKerell,A.D.J., Bashford,D., Bellott,R.L., Dunbrack,R.L., Jr., Evanseck,J.D., Field,M.J., Fischer,S., Gao,J., Guo,H., Ha,S. et al. (1998) All-Atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B., 102, 3586-3616.
20. Sali,A. and Overington,J.P. (1994) Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci., 3, 1582-1596.
21. Pearson,W.R. (2000) Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol., 132, 185-219.
22. Pieper,U., Eswar,N., Stuart,A.C., Ilyin,V.A. and Sali,A. (2002) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res., 30, 255-259.
23. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
24. Schaffer,A.A., Wolf,Y.I., Ponting,C.P., Koonin,E.V., Aravind,L. and Altschul,S.F. (1999) IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, 15, 1000-1011.
25. Melo,F., Sanchez,R. and Sah,A. (2002) Statistical potentials for fold assessment. Protein Sci., 11, 430-448.
26. Sanchez,R. and Sali,A. (1999) ModBase: a database of comparative protein structure models. Bioinformatics, 15, 1060-1061.
27. Sanchez,R., Pieper,U., Mirkovic,N., de Bakker,P.I., Wittenstein,E. and Sali,A. (2000) MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res., 28, 250-253.
28. Benson,D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J., Rapp,B.A. and Wheeler,D.L. (2002) GenBank. Nucleic Acids Res., 30, 17-20.
29. Pearl,F.M., Bennett,C.F., Bray,J.E., Harrison,A.P., Martin,N., Shepherd,A., Sillitoe,I., Thornton,J. and Orengo,C.A. (2003) The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res., 31, 452-455.
30. Bateman,A., Birney,E., Cerruti,L., Durbin,R., Etwiller,L., Eddy,S.R., Griffiths-Jones,S., Howe,K.L., Marshall,M. and Sonnhammer,E.L. (2002) The Pfam protein families database. Nucleic Acids Res., 30, 276-280.
31. Servant,F., Bru,C., Carrere,S., Courcelle,E., Gouzy,J., Peyruc,D. and Kahn,D. (2002) ProDom: automated clustering of homologous domains. Brief. Bioinform., 3, 246-251.
32. Ilyin,V.A., Pieper,U., Stuart,A.C., Marti-Renom,M.A., McMahan,L. and Sali,A. (2003) ModView, visualization of multiple protein sequences and structures. Bioinformatics, 19, 165-166.
33. Sippl,M.J. (1993) Recognition of errors in three-dimensional structures of proteins. Proteins, 17, 355-362.
34. Ilyin,V.A. (1994) Non-polar nuclei in fungal microbial RNases. Protein Eng., 7, 1189-1195.
35. Sayle,R.A. and Milner-White,E.J. (1995) RASMOL: biomolecular graphics for all. Trends Biochem. Sci., 20, 374.
36. Henikoff,J.G. and Henikoff,S. (1996) Using substitution probabilities to improve position-specific scoring matrices. Comput. Appl. Biosci., 12, 135-143.
37. Stuart,A.C., Ilyin,V.A. and Sali,A. (2002) LigBase: a database of families of aligned ligand binding sites in known protein sequences and structures. Bioinformatics, 18, 200-201.
38. Marti-Renom,M.A., Ilyin,V.A. and Sali,A. (2001) DBAli: a database of protein structure alignments. Bioinformatics, 17, 746-747.