ESyPred3D: Prediction of proteins 3D structures

Bioinformatics

Volumn 18, Issue 9, 2002, Pages 1250-1256

  Lambert, Christophe ^a   Léonard, Nadia ^a   De Bolle, Xavier ^a   Depiereux, Eric ^a  

^a UNIVERSITY OF NAMUR   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; MOLECULAR MODEL; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; RAT; SCORING SYSTEM; SEQUENCE ANALYSIS; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; THREE DIMENSIONAL IMAGING;

EID: 0036740806     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.9.1250     Document Type: Article

References (30)

1. Altschul,S.F., Madden,T.L., Schäffer,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.
2. Briffeuil,P., Baudoux,G., Reginster,I., De Bolle,X., Vinals,C., Feytmans,E. and Depiereux,E. (1998) Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance predictions reliability. Bioinformatics, 14, 357-366.
3. Browne,W.J., North,A.C. and Phillips,D.C. (1969) A possible three-dimensional structure of bovine alpha-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol., 42, 65-86.
4. Corpet,F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
5. Depiereux,E., Baudoux,G., Briffeuil,P., Reginster,I., De Bolle,X., Vinals,C. and Feytmans,E. (1997) Match-Box server: a multiple sequence alignment tool placing emphasis on reliability. Comput. Appl. Biosci., 13, 249-256.
6. Depiereux,E. and Feytmans,E. (1992) Match-Box: a fundamentally new algorithm for simultaneous alignment of several protein sequences. Comput. Appl. Biosci., 8, 501-509.
7. Eisenhaber,F., Persson,B. and Argos,P. (1995) Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence. Crit. Rev. Biochem. Mol. Biol., 30, 1-94.
8. 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.
9. Fischer,D., Barret,C., Bryson,K., Elofsson,A., Godzik,A., Jones,D., Karplus,K.J., Kelley,L.A., MacCallum,R.M., Pawowski,K., Rost,B., Rychlewski,L. and Sternberg,M. (1999) CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins, (Suppl 3), 209-217.
10. Gotoh,O. (1996) Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinement as Assessed by Reference to Structural Alignments. J. Mol. Biol., 264, 823-838.
11. Kann,M., Qian,B. and Goldstein,R.A. (2000) Optimization of a new score function for the detection of remote homologs. Proteins, 41, 498-503.
12. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
13. Karplus,K., Sjolander,K., Barrett,C., Cline,M., Haussler,D., Hughey,R., Holm,L. and Sander,C. (1997) Predicting protein structure using hidden Markov models. Proteins, (Suppl 1), 134-139.
14. Laskowski,R.A., Moss,D.S. and Thornton,J.M. (1993) Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol., 231, 1049-1067.
15. Luthy,R., Bowie,J.U. and Eisenberg,D. (1992) Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
16. Martin,A.C., MacArthur,M.W. and Thornton,J.M. (1997) Assessment of comparative modeling in CASP2. Proteins, (Suppl 1), 14-28.
17. Melo,F. and Feytmans,E. (1997) Novel Knowledge-based Mean Force Potential at Atomic Level. J. Mol. Biol., 267, 207-222.
18. Morgenstern,B. (1999) DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 15, 211-218.
19. Mosimann,S., Meleshko,R. and James,M.N. (1995) A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins, 23, 301-317.
20. Neuwald,A.F., Liu,J.S. and Lawrence,C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
21. Rost,B. and O'Donoghue,S. (1997) Sisyphus and prediction of protein structure. Comput. Appl. Biosci., 13, 345-356.
22. Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
23. Sali,A., Sanchez,R. and Badretdinov,A. (1997) MODELLER: A Program for Protein Structure Modeling Release 4.
24. Sanchez,R. and Sali,A. (1997) Advances in comparative protein-structure modeling. Curr Opin. Struct. Biol., 7, 206-214.
25. Thompson,J.D., Higgins,D.G. and Gibson,T.J. (1994) CLUSTALw: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
26. Thompson,J.D., Plewniak,F. and Poch,O. (1999) A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res., 27, 2682-2690.
27. Tramontano,A. (1998) Homology modeling with low sequence identity. Methods, 14, 293-300.
28. Venclovas,C., Zemla,A., Fidelis,K. and Moult,J. (1999) Some measures of comparative performance in the three CASPs. Proteins, (Suppl 3), 231-237.
29. Yang,A.S. and Honig,B. (1999) Sequence to structure alignment in comparative modeling using PrISM. Proteins, (Suppl 3), 66-72.
30. Zemla,A. (2000) LGA program: A Method for Finding 3D Similarities in Protein Structures. Accessed at http://PredictionCenter.llnl.gov/local/lga.