Homology modeling of membrane proteins: A critical assessment

Computational Biology and Chemistry

Volumn 30, Issue 2, 2006, Pages 120-126

  Reddy, Ch Surendhar ^a   Vijayasarathy, K ^a   Srinivas, E ^a   Sastry, G Madhavi ^a   Sastry, G Narahari ^a  

^a INDIAN INSTITUTE OF CHEMICAL TECHNOLOGY   (India)

Author keywords

3 Dimensional structure; Fold; Homology modeling; Low sequence identity; Membrane proteins; Stereochemical quality; Structural similarity

Indexed keywords

FOLD; HOMOLOGY MODELING; LOW SEQUENCE IDENTITY; STEREOCHEMICAL QUALITY; STRUCTURAL SIMILARITY;

DRUG PRODUCTS; MATHEMATICAL MODELS; MEMBRANES; STEREOCHEMISTRY; TARGETS; THREE DIMENSIONAL;

PROTEINS;

MEMBRANE PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN DATABASE; SEQUENCE ALIGNMENT; STATISTICS; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; MEMBRANE PROTEINS; MODELS, MOLECULAR; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33645843948     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2005.12.002     Document Type: Article

References (34)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Bates P.A., Kelley L.A., MacCallum R.M., and Sternberg M.J. Enhancement of protein modelling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins 5 Suppl. (2001) 39-46
4. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
5. +-ATPase: a comparative protein modeling study. Biochem. Biophys. Res. Commum. 319 (2004) 312-320
6. Briffeuil P., Baudoux G., Lambert C., De Bolle X., Vinals C., Feytmans E., and Depiereux E. Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions. Bioinformatics 14 (1998) 357-366
7. Bujnicki J.M., Elofsson A., Fischer D., and Rychlewski L. LiveBench-1: continuous benchmarking of protein structure prediction servers. Protein Sci. 10 (2001) 352-361
8. Carugo O., and Pongor S. A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci. 10 (2001) 1470-1473
9. Contreras-Moreira B., and Bates P.A. Domain fishing: a first step in protein comparative modelling. Bioinformatics 18 (2002) 1141-1142
10. Dayringer H.E., Tramontano A., and Fletterick R.J. Interactive program for visualization and modelling of proteins, nucleic acids and small molecules. J. Mol. Graph. 4 (1986) 82-87
11. Dunbrack Jr. R.L. Rotamer libraries in the 21st century. Curr. Opin. Struct. Biol. 12 (2002) 431-440
12. Eisenberg D., Lüthy R., and Bowie J.U. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol. 277 (1997) 396-404
13. Elofsson A. A study on protein sequence alignment quality. Proteins: Struct. Funct. Genet. 46 (2002) 330-339
14. Fischer D., Barret C., Bryson K., Elofsson A., Godzik A., Jones D., Karplus K.J., Kelley L.A., MacCallum R.M., and Pawlowski K. CAFASP-1: critical assessment of fully automated structure prediction methods. Proteins 3 Suppl. (1999) 209-217
15. Guex N., and Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 18 (1997) 2714-2723
16. Jones D.T. Protein secondary structure prediction based on position specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
17. Kelly, K., 1999. 3D bioinformatics and comparative protein modeling in MOE, J. Chem. Comp. Group, autumn ed.
18. Levitt M., and Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 5913-5920
19. Lovell S.C., Davis I.W., Arendall W.B., de Bakker P.I., Word J.M., Prisant M.G., Richardson J.S., and Richardson D.C. Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins 50 (2003) 437-450
20. Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 356 (1992) 83-85
21. Mosimann S., Meleshko R., and James M.N.G. A critical assessment of comparative molecular modeling of tertiary structures of proteins. Proteins: Struct. Funct. Genet. 23 (1995) 301-317
22. Moult J., Hubbard T., Fidelis K., and Pedersen J.T. Critical assessment of methods of protein structure prediction (CASP): round III. Proteins 3 Suppl. (1999) 2-6
23. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amno acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
24. Sali A., and Blundell T.L. Comparative protein modeling of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
25. Sanchez R., and Sali A. Advances in comparative protein-structure modelling. Curr. Opin. Struct. Biol. 7 (1997) 206-214
26. Sanchez R., Pieper U., Melo F., Eswar N., Marti-Renom M.A., Madhusudhan M.S., Mirkovic N., and Sali A. Protein structure modeling for structural genomics. Nat. Struct. Biol. 7 Suppl. (2000) 986-990
27. Schwede T., Kopp J., Guex N., and Peitsch M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31 (2003) 3381-3385
28. Sippl M.J. Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures. J. Comp. Aid. Mol. Des. 7 (1993) 473-501
29. Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 17 (1993) 355-362
30. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighing, position specific gap penalties and weight matrix choice. Nucleic Acids Res. l22 (1994) 4673-4680
31. Tusnády G.E., Dosztányi Z., and Simon I. PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank. Nucleic Acids Res. 33 (2005) 275-278
32. Wallace B.A., Cascio M., and Mielke D.L. Evaluation of methods for the prediction of membrane protein secondary structures. Proc. Natl. Acad. Sci. U.S.A. 83 (1986) 9423-9427
33. Wallner B., and Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci. 14 (2005) 1315-1327
34. Zhang Y., and Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 57 (2004) 702-710