Parmodel: A web server for automated comparative modeling of proteins

Biochemical and Biophysical Research Communications

Volumn 325, Issue 4, 2004, Pages 1481-1486

  Uchôa, Hugo Brandão ^a   Jorge, Guilherme Eberhart ^a   Freitas Da Silveira, Nelson José ^a   Camera Jr , João Carlos ^a   Canduri, Fernanda ^a,b   De Azevedo Jr , Walter Filgueira ^a,b  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b INSTITUTO BUTANTAN   (Brazil)

Author keywords

Bioinformatics; Comparative modeling; Structural analysis

Indexed keywords

ARTICLE; AUTOMATION; BIOINFORMATICS; COMPUTER PROGRAM; CRYSTALLOGRAPHY; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE;

ALGORITHMS; COMPUTER SIMULATION; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; INTERNET; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 8844259837     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.10.192     Document Type: Article

References (42)

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
2. D. Baker, and A. Sali Protein structure prediction and structural genomics Science 294 2001 93 96
3. M.A. Marti-Renom, A.C. Stuart, A. Fiser, R. Sanchez, F. Melo, and A. Sali Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 29 2000 291 325
4. D. Vitkup, E. Melamud, J. Moult, and C. Sander Completeness in structural genomics Nat. Struct. Biol. 8 2001 559 566
5. W. Filgueira de Azevedo Jr., R.T. Gaspar, F. Canduri, J.C. Camera Jr., and N. Freitas da Silveira Molecular model of cyclin-dependent kinase 5 complexed with roscovitine Biochem. Biophys. Res. Commun. 297 2002 1154 1158
6. J.H. Pereira, F. Canduri, J.S. de Oliveira, N.J. Silveira, L.A. Basso, M.S. Palma, W.F. de Azevedo, and D.S. Santos Structural bioinformatics study of EPSP synthase from Mycobacterium tuberculosis Biochem. Biophys. Res. Commun. 312 2003 608 614
7. N.J. da Silveira, H.B. Uchoa, F. Canduri, J.H. Pereira, J.C. Camera Jr., L.A. Basso, M.S. Palma, D.S. Santos, and W.F. de Azevedo Jr. Structural bioinformatics study of PNP from Schistosoma mansoni Biochem. Biophys. Res. Commun. 322 2004 100 104
8. A. Tramontano, R. Leplae, and V. Morea Analysis and assessment of comparative modeling predictions in CASP4 Proteins 45 2001 22 38
9. R. Sanchez, and A. Sali Large-scale protein structure modeling of the Saccharomyces cerevisiae genome Proc. Natl Acad. Sci. 95 1998 13597 13602
10. N. Eswar, B. John, N. Mirkovic, A. Fiser, V.A. Ilyin, U. Pieper, A.C. Stuart, M.A. Marti-Renom, M.S. Madhusudhan, B. Yerkovich, and A. Sali Tools for comparative protein structure modeling and analysis Nucleic Acids Res. 31 2003 3375 3380
11. P.E. Bourne, and H. Weissig Structural Bioinformatics ss First ed. 2003 Wiley-Liss New York 509 524
12. O. Lund, K. Frimand, J. Gorodkin, H. Bohr, J. Bohr, J. Hansen, and S. Brunak Protein distance constraints predicted by neural networks and probability density functions Protein Eng. 10 1997 1241 1248
13. T. Schwede, J. Kopp, N. Guex, and M.C. Peitsch SWISS-MODEL: an automated protein homology-modeling server Nucleic Acids Res. 31 2003 3381 3385
14. C. Lambert, N. Leonard, X. De Bolle, and E. Depiereux ESyPred3D: prediction of proteins 3D structures Bioinformatics 18 2002 1250 1256
15. P.A. Bates, L.A. Kelley, R.M. MacCallum, and M.J. Sternberg Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM Proteins 45 2001 39 46
16. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815
17. A. Fiser, R.K. Do, and A. Sali Modeling of loops in protein structures Protein Sci. 9 2000 1753 1773
18. A.D. MacKerell Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher III, B. Roux, M. Schlenkrich, J.C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, and M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616
19. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
20. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402
21. K.M. Chao, W.R. Pearson, and W. Miller Aligning two sequences within a specified diagonal band Comput. Appl. Biosci. 8 1992 481 487
22. T. Ohlson, B. Wallner, and A. Elofsson Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods Proteins 57 2004 188 197
23. M.A. Marti-Renom, M.S. Madhusudhan, and A. Sali Alignment of protein sequences by their profiles Protein Sci. 13 2004 1071 1087
24. R.W. Hooft, G. Vriend, C. Sander, and E.E. Abola Errors in protein structures Nature 381 1996 272
25. R.A. Laskowski, M.W. MacArthur, D.S. Moss, and J.M. Thornton PROCHECK-a program to check the stereochemical quality of protein structures J. Appl. Cryst. 26 1993 283 291
26. EU 3-D Validation Network, Who checks the checkers? Four validation tools applied to eight atomic resolution structures, J. Mol. Biol. 276 (1998) 417-436
27. J.U. Bowie, R. Luthy, and D. Eisenberg A method to identify protein sequences that fold into a known three-dimensional structure Science 256 1991 164 170
28. R. Luthy, J.U. Bowie, and D. Eisenberg Assessment of protein models with three-dimensional profiles Nature 356 1992 383 385
29. W.F. Van Gunsteren, S.R. Billeter, A. Eising, P.H. Hünenberger, P. Krüger, A.E. Mark, W.R.P. Scott, and I.G. Tironi Biomolecular Simulations: The GROMOS96 Manual and User Guide 1996 VdF Hochschulverlag ETHZ Zurich
30. H.J.C. Berendsen, D. Van der Spoel, and R. Van Drunen GROMACS: a message-passing parallel molecular dynamics implementation Comp. Phys. Commun. 91 1995 43 56
31. E. Lindahl, B. Hess, and D. Van der Spoel GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Mod. 7 2001 306 317
32. P. Koehl, and M. Levitt A brighter future for protein structure prediction Nat. Struct. Biol. 6 1999 108 111
33. J. Moult The current state of the art in protein structure prediction Curr. Opin. Biotechnol. 7 1996 422 427
34. J.A. Flohil, G. Vriend, and H.J. Berendsen Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis Proteins 48 2002 593 604
35. D.J. Bacon, and W.F. Anderson A fast algorithm for rendering space-filling molecule pictures J. Mol. Graphics 6 1988 219 220
36. E.A. Merritt Raster3D Version 2.0. A program for photorealistic molecular graphics Acta Crystallogr. 50 1994 869 873
37. P.J. Kraulis MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24 1991 946 950
38. Y. Zhang, J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins (2004) [Epub ahead of print]
39. A. Zemla, C. Venclovas, J. Moult, and K. Fidelis Processing and analysis of CASP3 protein structure predictions Proteins 3 1999 22 29
40. N. Siew, A. Elofsson, L. Rychlewski, and D. Fischer MaxSub: an automated measure for the assessment of protein structure prediction quality Bioinformatics 16 2000 776 785
41. M. Levitt, and M. Gerstein A unified statistical framework for sequence comparison and structure comparison Proc. Natl. Acad. Sci. USA 95 1998 5913 5920
42. M. Gerstein, and M. Levitt Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures Proc. Int. Conf. Intell. Syst. Mol. Biol. 4 1996 59 67