Comparative Protein Structure Modeling in Genomics

Journal of Computational Physics

Volumn 151, Issue 1, 1999, Pages 388-401

  Sánchez, Roberto ^a   Šali, Andrej ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

3D MODELING; GENES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PIPELINES; PROTEINS; X RAY CRYSTALLOGRAPHY;

3D STRUCTURE; DETERMINATION OF PROTEINS; GENOME PROJECTS; GENOMICS; LARGE-SCALES; MODELLING TECHNIQUES; PROTEIN SEQUENCES; PROTEINS STRUCTURES; STRUCTURE MODELS; THREE DIMENSIONAL (3D) STRUCTURES;

GENOME;

EID: 0042624145     PISSN: 00219991     EISSN: None     Source Type: Journal    
DOI: 10.1006/jcph.1999.6200     Document Type: Article

References (75)

1. Oliver S. G. From DNA sequence to biological function. Nature. 379:1996;597.
2. Koonin E. V., Mushegian A. R. Complete genome sequences of cellular life forms: Glimpses of theoretical evolutionary genomics. Curr. Opin. Gen. Dev. 6:1996;757.
3. Dujon B. The yeast genome project: What did we learn? Trends Genet. 12:1996;263.
4. Bork P., Dandekar T., Diaz-Lazcoz Y., Eisenhaber F., Huynen M., Yuan Y. Predicting function: From genes to genomes and back. J. Mol. Biol. 283:1998;707.
5. Šali A. 100,000 protein structures for the biologist. Nature Struct. Biol. 5:1998;1029.
6. Abola E. E., Bernstein F. C., Bryant S. H., Koetzle T. F., Weng J. Protein data bank. Crystallographic Databases - Information, Content, Software Systems, Scientific Applications. 1987;107-132.
7. Johnson M. S., Srinivasan N., Sowdhamini R., Blundell T. L. Knowledge-based protein modelling. CRC Crit. Rev. Biochem. Mol. Biol. 29:1994;1.
8. Rychlewski L., Zhang B., Godzik A. Fold and function predictions for mycoplasma genitalium proteins. Fold. Des. 3:1998;229.
9. Huynen M., Doerks T., Eisenhaber F., Orengo C., Sunyaev S., Yuan Y., Bork P. Homology-based fold predictions for mycoplasma genitalium proteins. J. Mol. Biol. 280:1998;323.
10. Bajorath J., Stenkamp R., Aruffo A. Knowledge-based model building of proteins: Concepts and examples. Protein Sci. 2:1994;1798.
11. Šali A. Modelling mutations and homologous proteins. Curr. Opin. Biotech. 6:1995;437.
12. Rost B., Sander C. Bridging the protein sequence-structure gap by structure predictions. Annu. Rev. Biophys. Biomol. Struct. 25:1996;113.
13. Sánchez R., Šali A. Advances in comparative protein-structure modeling. Curr. Opin. Struct. Biol. 7:1997;206.
14. Lesk A. M., Chothia C. H. The response of protein structures to amino-acid sequence changes. Philos. Trans. R. Soc. London Ser. B. 317:1986;345.
15. Hubbard T. J. P., Blundell T. L. Comparison of solvent inaccessible cores of homologous proteins: Definitions useful for protein modelling. Protein Eng. 1:1987;159.
16. Dunbrack R. L. Jr., Gerloff D. L., Bower M., Chen X., Lichtarge O., Cohen F. E. Meeting review: The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar California, December 13-16, 1996. Folding & Design. 2:1997;R27.
17. Moult J., Hubbard T., Bryant S. H., Fidelis K., Pedersen J. T. Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins. 1:1997;2.
18. Lesk A. CASP2: Report on ab initio predictions. Proteins. 1:1997;151.
19. Jones D. T. Progress in protein structure prediction. Curr. Opin. Struct. Biol. 7:1997;377.
20. Browne W. J., North A. C. T., Phillips D. C., Brew K., Vanaman T. C., Hill R. C. A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol. 42:1969;65.
21. Greer J. Comparative model-building of the mammalian serine proteases. J. Mol. Biol. 153:1981;1027.
22. Blundell T. L., Sibanda B. L., Sternberg M. J. E., Thornton J. M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326:1987;347.
23. Jones T. H., Thirup S. Using known substructures in protein model building and crystallography. EMBO J. 5:1986;819.
24. Unger R., Harel D., Wherland S., Sussman J. L. A 3-D building blocks approach to analyzing and predicting structure of proteins. Proteins. 5:1989;355.
25. Claessens M., Cutsem E. V., Lasters I., Wodak S. Modelling the polypeptide backbone with "spare parts" from known protein structures. Protein Eng. 4:1989;335.
26. Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 226:1992;507.
27. Havel T. F., Snow M. E. A new method for building protein conformations from sequence alignments with homologues of known structure. J. Mol. Biol. 217:1991;1.
28. Srinivasan S., March C. J., Sudarsanam S. An automated method for modeling proteins on known templates using distance geometry. Protein Sci. 2:1993;227.
29. Šali A., Blundell T. L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779.
30. Borchert T. V., Abagyan R. A., Kishan K. V. R., Zeelen J. P., Wierenga R. K. The crystal structure of an engineered monomeric triosephosphate isomerase, monotim: The correct modelling of an eight residue loop. Structure. 1:1993;205.
31. van Vlijmen H. W. T., Karplus M. PDB-based protein loop prediction: Parameters for selection and methods for optimization. J. Mol. Biol. 267:1997;975.
32. Eisenmenger F., Argos P., Abagyan R. A method to configure protein side-chains from the main-chain trace in homology modelling. J. Mol. Biol. 231:1993;849.
33. Vásquez M. Modeling side-chain conformation. Curr. Opin. Str. Biol. 6:1996;217.
34. Peitsch M. C., Wilkins M. R., Tonella L., Sánchez J. C., Appel R. D., Hochstrasser D. F. Large-scale protein modelling and integration with the SWISS-PROT and SWISS-2DPAGE databases: The example ofEscherichia coli. Electrophoresis. 18:1997;498.
35. Peitsch M. C. Promod and swiss-model - Internet-based tools for automated comparative protein modeling. Biochem. Soc. Trans. 24:1996;274.
36. Sánchez R., Sali A. Large-scale protein structure modeling of theSaccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 95:1998;13597.
37. Sippl M. J. Recognition of errors in three-dimensional structures of proteins. Proteins. 17:1993;355.
38. Pearson W. R. Rapid and sensitive comparison with FASTA and FASTP. Methods Enzymol. 183:1990;63.
39. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 215:1990;403.
40. Needleman S. B., Wunsch C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443.
41. Smith T. F., Waterman M. S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195.
42. Bowie J. U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164.
43. Jones D. T., Taylor W. R., Thornton J. M. A new approach to protein fold recognition. Nature. 358:1992;86.
44. Godzik A., Kolinski A., Skolnick J. Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol. 227:1992;227.
45. Krogh A., Brown M., Mian I. S., Sjolander K., Haussler D. Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol. 235:1994;1501.
46. Sonnhammer E. L. L., Eddy S. R., Durbin R. Pfam, A comprehensive database of protein domain families based on seed alignments. Proteins. 28:1997;405.
47. Eddy S. R. Hidden Markov models. Curr. Opin. Struct. Biol. 6:1996;361.
48. Altschul S. F., Madden T. L., Schaffer A. A., Zhang Zhang J., Miller W., Lipman D. J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389.
49. Altschul S. F., Gish W. Local alignment statistics. Methods Enzymol. 266:1996;460.
50. Fischer D., Eisenberg D. Assigning folds to the proteins encoded by the genome ofMycoplasma genitalium. Proc. Natl. Acad. Sci. U.S.A. 94:1997;11929.
51. Levitt M. Competitive assessment of protein fold recognition and alignment accuracy. Proteins. 1:1997;92.
52. Koretke K. K., Luthey-Schulten Z., Wolynes P. G. Self-consistently optimized statistical mechanical energy functions for sequence structure alignment. Protein Sci. 5:1996;1043.
53. Lesk A. M., Levitt M., Chothia C. Alignment of the amino acid sequences of distantly related proteins using variable gap penalties. Protein Eng. 1:1986;77.
54. Sánchez R., Šali A. Evaluation of comparative protein structure modeling by MODELLER-3. Proteins. 1:1997;50.
55. Guenther B., Onrust R., Şali A., O'Donnell M., Kuriyan J. Crystal structure of the δ′ subunit of the clamp-loader complex ofE. coli. Cell. 91:1997;335.
56. Faber H. R., Matthews B. W. A mutant T4 lysozyme displays five different crystal conformations. Nature. 348:1990;263.
57. Pawlowski K., Bierzyński A., Godzik A. Structural diversity in a family of homologous proteins. J. Mol. Biol. 258:1996;349.
58. Orengo C. A., Jones D. T., Thornton J. M. Protein superfamilies and domain superfolds. Nature. 372:1994;631.
59. Matsumoto R., Šali A., Ghildyal N., Karplus M., Stevens R. L. Packaging of proteases and proteoglycans in the granules of mast cells and other hematopoietic cells. A cluster of histidines in mouse mast cell protease-7 regulates its binding to heparin serglycin proteoglycan. J. Biol. Chem. 270:1995;19524.
60. Xu L. Z., Sánchez R., Šali A., Heintz N. Ligand specificity of brain lipid binding protein. J. Biol. Chem. 271:1996;24711.
61. Bairoch A. PROSITE: A dictionary of sites and patterns in proteins. Nucl. Acids Res. 20:1992;2013.
62. Pawson T. Protein modules and signalling networks. Nature. 373:1995;573.
63. Wallace A. C., Borkakoti N., Thornton J. M. TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites. Protein Sci. 6:1997;2308.
64. 1. J. Mol. Biol. 281:1998;949.
65. Chothia C., Lesk A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823.
66. Ring C. S., Sun E., McKerrow J. H., Lee G. K., Rosenthal P. J., Kuntz I. D., Cohen F. E. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc. Natl. Acad. Sci. U.S.A. 90:1993;3583.
67. Totrov M., Abagyan R. Detailedab initio. Nature Struct. Biol. 1:1994;259.
68. Vakser I. A. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins. 1:1997;226.
69. Holm L., Sander C. Mapping the protein universe. Science. 273:1996;595.
70. Mewes H. W., Albermann K., Bähr M., Frishman D., Gleissner A., Hani J., Heumann K., Kleine K., Maierl A., Oliver S. G., Pfeiffer F., Zollner A. Overview of the yeast genome. Nature. 387:1997;7-65.
71. Altschul S. F. Generalized affine gap costs for protein sequence alignment. Proteins. 32:1998;88.
72. Brooks B. R., Bruccoleri R. E., Olafson B. D., States D. J., Swaminathan S., Karplus M. CHARMM: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4:1983;187.
73. Teichmann S. A., Park J., Chothia C. Structural assignments to theMycoplasma genitalium. Proc. Natl. Acad. Sci. U.S.A. 22:1998;14658.
74. Grandori R. Systematic fold recognition analysis of the sequences encoded by the genome. Mycoplasma pneumoniae, Protein Eng. 11:1998;1129.
75. Hubbard T. J. P., Ailey B., Brenner S. E., Murzin A. G., Chothia C. SCOP: A structural classification of proteins database. Nuc. Acids Res. 27:1999;254.