Microbial Genomes Have over 72% Structure Assignment by the Threading Algorithm PROSPECTOR_Q

Proteins: Structure, Function and Genetics

Volumn 55, Issue 2, 2004, Pages 464-473

  Kihara, Daisuke ^a   Skolnick, Jeffrey ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

Fold distribution; Genome scale protein structure prediction; Protein function prediction; Threading

Indexed keywords

ALGORITHM; ARTICLE; GENE SEQUENCE; GENOME; MICROBIAL GENETICS; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; GENOME, BACTERIAL; GENOME, FUNGAL; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEIN CONFORMATION; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 1842479856     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20044     Document Type: Article

References (61)

1. Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res 2002;30:42-46.
2. Burley SK. An overview of structural genomics. Nat Struct Biol 2000;7 Suppl:932-934.
3. Skolnick J, Fetrow JS, Kolinski A. Structural genomics and its importance for gene function analysis. Nat Biotechnol 2000;18:283-287.
4. Fetrow JS, Godzik A, Skolnick J. Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: identification of proteins exhibiting the glutare-doxin/thioredoxin disulfide oxidoreductase activity. J Mol Biol 1998;282:703-711.
5. Zhang L, Godzik A, Skolnick J, Fetrow JS. Functional analysis of the Escherichia coli genome for members of the alpha/beta hydrolase family. Fold Des 1998;3:535-548.
6. Kihara D, Zhang Y, Lu H, Kolinski A, Skolnick J. Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci USA 2002;99:5993-5998.
7. Sanchez R, Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc Natl Acad Sci USA 1998;95:13597-13602.
8. Yamaguchi A, Iwadate M, Suzuki E, Yura K, Kawakita S, Umeyama H, Go M. Enlarged FAMSBASE: protein 3D structure models of genome sequences for 41 species. Nucleic Acids Res 2003;31:463-468.
9. Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002;49:350-364.
10. Lu L, Arakaki AK, Lu H, Skolnick J. Multimeric Threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res 2003;13:1146-1154.
11. Smith GR, Sternberg MJ. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
12. Vajda S, Vakser IA, Sternberg MJ, Janin J. Modeling of protein interactions in genomes. Proteins 2002;47:444-446.
13. Jones DT. Protein structure prediction in the postgenomic era. Curr Opin Struct Biol 2000;10:371-379.
14. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
15. Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000;9:232-241.
16. Eddy SR. Hidden Markov models. Curr Opin Struct Biol 1996;6:361-365.
17. Bateman A, Birney E, Cerruti L, Durbin R, Etwiller L, Eddy SR, Griffiths-Jones S, Howe KL, Marshall M, Sonnhammer EL. The Pfam protein families database. Nucleic Acids Res 2002;30:276-280.
18. Karplus K, Barrett C, Hughey R. Hidden Markov models for detecting remote protein homologies. Bioinformatics 1998;14:846-856.
19. Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331.
20. Skolnick J, Zhang Y, Arakaki AK, Kolinski A, Boniecki M, Szilagyi A, Kihara D. TOUCHSTONE: a unified approach to protein structure prediction. Proteins 2003;53:469-479.
21. Fischer D, Eisenberg D. Assigning folds to the proteins encoded by the genome of Mycoplasma genitalium. Proc Natl Acad Sci USA 1997;94:11929-11934.
22. 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 1998;280:323-326.
23. Teichmann SA, Park J, Chothia C. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci USA 1998;95:14658-14663.
24. Rychlewski L, Zhang B, Godzik A. Fold and function predictions for Mycoplasma genitalium proteins. Fold Des 1998;3:229-238.
25. Wolf YI, Brenner, Steven, E., Bash, Paul A., & Koonin, Eugine V. Distribution of protein folds in the three superkingdoms of life. genome research 1999;9:17-26.
26. Muller A, MacCallum RM, Sternberg MJ. Benchmarking PSI-BLAST in genome annotation. J Mol Biol 1999;293:1257-1271.
27. Jones DT. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 1999;287:797-815.
28. Salamov AA, Suwa M, Orengo CA, Swindells MB. Genome analysis: Assigning protein coding regions to three-dimensional structures. Protein Sci 1999;8:771-777.
29. Skolnick J, Kihara D. Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm. Forthcoming 2003.
30. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
31. Frishman D, Mokrejs M, Kosykb D, Kastenmuller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K, Mewes HW. The PEDANT genome database. Nucleic Acids Res 2003;31:207-211.
32. Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N, Nishikawa K. GTOP: a database of protein structures predicted from genome sequences. Nucleic Acids Res 2002;30:294-298.
33. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - a hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
34. Skolnick J, Kolinski A, Ortiz A. Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 2000;38:3-16.
35. Karchin R, Cline M, Mandel-Gutfreund Y, Karplus K. Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry. Proteins 2003;51:504-514.
36. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
37. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003;31:365-370.
38. Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 1988;85:2444-2448.
39. Pearson WR. Empirical statistical estimates for sequence similarity searches. J Mol Biol 1998;276:71-84.
40. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
41. Bairoch A. The ENZYME database in 2000. Nucleic Acids Res 2000;28:304-305.
42. Bukhman YV, Skolnick J. BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics 2001;17:468-478.
43. Hegyi H, Lin J, Greenbaum D, Gerstein M. Structural genomics analysis: characteristics of atypical, common, and horizontally transferred folds. Proteins 2002;47:126-141.
44. Kihara D, Lu H, Kolinski A, Skolnick J. TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci USA 2001;98:10125-10130.
45. Zhang Y, Skolnick J. Assembly of protein tertiary structures from substructures of weakly scoring threading templates. Forthcoming 2003.
46. Kihara D, Skolnick J. The PDB is a covering set of small protein structures. J Mol Biol 2003;334:793-802.
47. Lo Conte L, Brenner SE, Hubbard TJ, Chothia C, Murzin AG. SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res 2002;30:264-267.
48. Norin M, Sundstrom M. Structural proteomics: developments in structure-to-function predictions. Trends Biotechnol 2002;20:79-84.
49. Hofmann K, Bucher P, Falquet L, Bairoch A. The PROSITE database, its status in 1999. Nucleic Acids Res 1999;27:215-219.
50. Maher MJ, Xiao Z, Wilce MC, Guss JM, Wedd AG. Rubredoxin from Clostridium pasteurianum. Structures of G10A, G43A and G10VG43A mutant proteins. Mutation of conserved glycine 10 to valine causes the 9-10 peptide link to invert. Acta Crystallogr D Biol Crystallogr 1999;55:962-968.
51. Taylor AB, Czerwinski RM, Johnson WH, Jr., Whitman CP, Hackert ML. Crystal structure of 4-oxalocrotonate tautomerase inactivated by 2-oxo-3-pentynoate at 2.4 Å resolution: analysis and implications for the mechanism of inactivation and catalysis. Biochemistry 1998;37:14692-14700.
52. Madan Babu M, Teichmann SA. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 2003;31:1234-1244.
53. Kolinski A, Betancourt MR, Kihara D, Rotkiewicz P, Skolnick J. Generalized comparative modeling (GENECOMP): A combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 2001;44:133-149.
54. Wojciechowski M, Skolnick J. Docking of small ligands to low-resolution and theoretically predicted receptor structures. J Comput Chem 2002;23:189-197.
55. Hegyi H, Gerstein M. The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. J Mol Biol 1999;288:147-164.
56. Wolf YI, Brenner SE, Bash PA, Koonin EV. Distribution of protein folds in the three superkingdoms of life. Genome Res 1999;9:17-26.
57. Rychlewski L, Zhang B, Godzik A. Functional insights from structural predictions: analysis of the Escherichia coli genome. Protein Sci 1999;8:614-624.
58. Martin AC, Orengo CA, Hutchinson EG, Jones S, Karmirantzou M, Laskowski RA, Mitchell JB, Taroni C, Thornton JM. Protein folds and functions. Structure 1998;6:875-884.
59. Myers EW, Miller W. Optimal alignments in linear space. Comput Appl Biosci 1988;4:11-17.
60. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
61. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.