Connecting the protein structure universe by using sparse recurring fragments

Structure

Volumn 13, Issue 8, 2005, Pages 1213-1224

  Friedberg, Iddo ^a   Godzik, Adam ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; CORRELATION ANALYSIS; EVOLUTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

PEPTIDE LIBRARY; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 23444459516     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2005.05.009     Document Type: Article

References (34)

1. S.E. Brenner, P. Koehl, and M. Levitt The ASTRAL compendium for protein structure and sequence analysis Nucleic Acids Res. 28 2000 254 256
2. E. Camon, D. Barrell, V. Lee, E. Dimmer, and R. Apweiler The Gene Ontology Annotation (GOA) Database-an integrated resource of GO annotations to the UniProt Knowledgebase In Silico Biol. 4 2004 5 6
3. I.G. Choi, J. Kwon, and S.H. Kim Local feature frequency profile: a method to measure structural similarity in proteins Proc. Natl. Acad. Sci. USA 101 2004 3797 3802
4. F. deMare, D.M. Kurtz Jr., and P. Nordlund The structure of Desulfovibrio vulgaris rubrerythrin reveals a unique combination of rubredoxin-like FeS4 and ferritin-like diiron domains Nat. Struct. Biol. 3 1996 539 546
5. K.F. Han, and D. Baker Global properties of the mapping between local amino acid sequence and local structure in proteins Proc. Natl. Acad. Sci. USA 93 1996 5814 5818
6. M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, S. Lewis, B. Marshall, and C. Mungall The Gene Ontology (GO) database and informatics resource Nucleic Acids Res. 32 2004 D258 D261
7. A. Harrison, F. Pearl, R. Mott, J. Thornton, and C. Orengo Quantifying the similarities within fold space J. Mol. Biol. 323 2002 909 926
8. N. Haspel, C.J. Tsai, H. Wolfson, and R. Nussinov Reducing the computational complexity of protein folding via fragment folding and assembly Protein Sci. 12 2003 1177 1187
9. J. Hou, G.E. Sims, C. Zhang, and S.H. Kim A global representation of the protein fold space Proc. Natl. Acad. Sci. USA 100 2003 2386 2390
10. T.J. Hubbard RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions Proteins Suppl 3 1999 15 21
11. L. Jaroszewski, L. Rychlewski, and A. Godzik Improving the quality of twilight-zone alignments Protein Sci. 9 2000 1487 1496
12. L. Jaroszewski, L. Rychlewski, Z. Li, W. Li, and A. Godzik FFAS03: a server for profile-profile sequence alignments Nucleic Acids Res. 1 2005 W284 W288
13. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
14. D. Kihara, and J. Skolnick The PDB is a covering set of small protein structures J. Mol. Biol. 334 2003 793 802
15. R. Kolodny, P. Koehl, L. Guibas, and M. Levitt Small libraries of protein fragments model native protein structures accurately J. Mol. Biol. 323 2002 297 307
16. W. Li, L. Jaroszewski, and A. Godzik Clustering of highly homologous sequences to reduce the size of large protein databases Bioinformatics 17 2001 282 283
17. P.W. Lord, R.D. Stevens, A. Brass, and C.A. Goble Investigating semantic similarity measures across the Gene Ontology: the relationship between sequence and annotation Bioinformatics 19 2003 1275 1283
18. P.W. Lord, R.D. Stevens, A. Brass, and C.A. Goble Semantic similarity measures as tools for exploring the gene ontology Pac. Symp. Biocomput. 2003 601 612
19. S. Misra, and J.H. Hurley Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p Cell 97 1999 657 666
20. A.G. Murzin, S.E. Brenner, T. Hubbard, and C. Chothia SCOP: a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247 1995 536 540
21. T. Noguchi, and Y. Akiyama PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003 Nucleic Acids Res. 31 2003 492 493
22. J.G. Omichinski, P.V. Pedone, G. Felsenfeld, A.M. Gronenborn, and G.M. Clore The solution structure of a specific GAGA factor-DNA complex reveals a modular binding mode Nat. Struct. Biol. 4 1997 122 132
23. C.A. Orengo, A.D. Michie, S. Jones, D.T. Jones, M.B. Swindells, and J.M. Thornton CATH-a hierarchic classification of protein domain structures Structure 5 1997 1093 1108
24. J.T. Pedersen, and J. Moult Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms Proteins 23 1995 454 460
25. M.G. Rossmann, and P. Argos Protein folding Annu. Rev. Biochem. 50 1981 497 532
26. L. Rychlewski, and A. Godzik Secondary structure prediction using segment similarity Protein Eng. 10 1997 1143 1153
27. L. Rychlewski, L. Jaroszewski, W. Li, and A. Godzik Comparison of sequence profiles. Strategies for structural predictions using sequence information Protein Sci. 9 2000 232 241
28. B.E. Shakhnovich, N.V. Dokholyan, C. DeLisi, and E.I. Shakhnovich Functional fingerprints of folds: evidence for correlated structure-function evolution J. Mol. Biol. 326 2003 1 9
29. B.E. Shakhnovich, J.M. Harvey, S. Comeau, D. Lorenz, C. DeLisi, and E. Shakhnovich ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations BMC Bioinformatics 4 2003 34
30. M.J. Sippl Superposition of three-dimensional objects: a fast and numerically stable algorithm for the calculation of the matrix optimal rotation Comput. Chem. 15 1991 73 78
31. C.J. Tsai, J.V. Maizel Jr., and R. Nussinov Anatomy of protein structures: visualizing how a one-dimensional protein chain folds into a three-dimensional shape Proc. Natl. Acad. Sci. USA 97 2000 12038 12043
32. R. Unger, D. Harel, S. Wherland, and J.L. Sussman A 3D building blocks approach to analyzing and predicting structure of proteins Proteins 5 1989 355 373
33. A. Velyvis, Y. Yang, C. Wu, and J. Qin Solution structure of the focal adhesion adaptor PINCH LIM1 domain and characterization of its interaction with the integrin-linked kinase ankyrin repeat domain J. Biol. Chem. 276 2001 4932 4939
34. Y. Ye, L. Jaroszewski, W. Li, and A. Godzik A segment alignment approach to protein comparison Bioinformatics 19 2003 742 749