Functional inferences from blind ab initio protein structure predictions

Journal of Structural Biology

Volumn 134, Issue 2-3, 2001, Pages 186-190

  Bonneau, Richard ^a   Tsai, Jerry ^a   Ruczinski, Ingo ^a   Baker, David ^a  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

Author keywords

CASP3; CASP4; Genomics; New folds; Rosetta

Indexed keywords

BACTERIOCIN;

PREDICTION; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS;

EID: 0035782683     PISSN: 10478477     EISSN: None     Source Type: Journal    
DOI: 10.1006/jsbi.2000.4370     Document Type: Article

References (34)

1. Bonneau, R., and Strauss, C. E. M. (2001) Improving the performance of ROSETTA using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins 43, 1-11.
2. Brenner, S. E., Chothia, C., and Hubbard, T. J. (1998) Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc. Natl. Acad. Sci. USA 95(11), 6073-6078.
3. Fetrow, J. S., Godzik, A., and Skolnick, J. (1998) Functional analysis of the Escherichia coli genome using the sequence-to-structure-to-function paradigm: Identification of proteins exhibiting the glutaredoxin/thioredoxin disulfide oxidoreductase activity. J. Mol. Biol. 282, 703-711.
4. Fetrow, J. S., Siew, N., and Skolnick, J. (1999) Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily. FASEB J. 13(13), 1866-1874.
5. Fetrow, J. S., and Skolnick, J. (1998) Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases. J. Mol. Biol. 281(5), 949-968.
6. Gonzalez, C., Langdon, G. M., Bruix, M., Galvez, A., Valdivia, E., Maqueda, M., and Rico, M. (2000) Bacteriocin AS-48, a microbial cyclic polypeptide structurally and functionally related to mammalian NK-lysin. Proc. Natl. Acad. Sci. USA 97(21), 11221-11226.
7. Holm, L., and Sander, C. (1995) Dali: A network tool for protein structure comparison. Trends Biochem. Sci. 20(11), 478-480.
8. Jonassen, I., Eidhammer, I., Grindhaug, S. H., and Taylor, W. R. (2000) Searching the protein structure databank with weak sequence patterns and structural constraints. J. Mol. Biol. 304, 599-619.
9. Lesk, A. M. (1997) CASP2: Report on ab initio predictions. Proteins Suppl. 1, 151-166.
10. Lo Conte, L., Ailey, B., Hubbard, T. J., Brenner, S. E., Murzin, A. G., and Chothia, C. (2000) SCOP: A structural classification of protein database. Nucleic Acids Res. 28(1), 257-259.
11. Martin, A. C., Orengo, C. A., Hutchinson, E. G., Jones, S., Karmirantzou, M., Laskowski, R. A., Mitchell, J. B., Taroni, C., and Thornton, J. M. (1998) Protein folds and functions. Structure 6(7), 875-884.
12. Mewes, H. W., Frishman, D., Gruber, C., Geier, B., Haase, D., Kaps, A., Lemcke, K., Mannhaupt, G., Pfeiffer, F., Schuller, C., Stocker, S., and Weil, B. (2000) MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 28(1), 37-40.
13. Moodie, S. L., Mitchell, J. B., and Thornton, J. M. (1996) Protein recognition of adenylate: An example of a fuzzy recognition template. J. Mol. Biol. 263, 486-500.
14. Moult, J., Hubbard, T., Bryant, S. H., Fidelis, K., and Pedersen, J. T. (1997) Critical assessment of methods of protein structure prediction (CASP): Round II. Proteins Suppl. 1, 2-6.
15. Moult, J., Hubbard, T., Fidelis, K., and Pedersen, J. T. (1999) Critical assessment of methods of protein structure prediction (CASP): Round III. Proteins Suppl. 3, 2-6.
16. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
17. Obmolova, G., Ban, C., Hsieh, P., and Yang, W. (2000) Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407(6805), 703-710.
18. Orengo, C. A., Bray, J. E., Hubbard, T., LoConte, L., and Sillitoe, I. (1999a) Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. Proteins Suppl. 3, 149-170.
19. Orengo, C. A., Todd, A. E., and Thornton, J. M. (1999b) From protein structure to function. Curr. Opin. Struct. Biol. 9(3), 374-382.
20. Ortiz, A. R., Kolinski, A., Rotkiewicz, P., Ilkowski, B., and Skolnick, J. (1999) Ab initio folding of proteins using restraints derived from evolutionary information. Proteins Suppl. 3, 177-185.
21. Ponting, C. P., and Russell, R. B. (1995) Swaposins: Circular permutations within genes encoding saposin homologues. Trends Biochem. Sci. 20(5), 179-180.
22. Rhee, S., Martin, R. G., Rosner, J. L., and Davies, D. R. (1998) A novel DNA-binding motif in MarA: The first structure for an AraC family transcriptional activator. Proc. Natl. Acad. Sci. USA 95(18), 10413-10418.
23. Russell, R. B., and Ponting, C. P. (1998) Protein fold irregularities that hinder sequence analysis. Curr. Opin. Struct. Biol. 8(3), 364-371.
24. Rychlewski, L., Zhang, B., and Godzik, A. (1998) Fold and function predictions for Mycoplasma genitalium proteins. Fold. Des. 3 (4), 229-238.
25. Samudrala, R., Xia, Y., Levitt, M., and Huang, E. S. (1999) A combined approach for ab initio construction of low resolution protein tertiary structures from sequence. Pac. Symp. Biocomput., 505-516.
26. Sanchez, R., and Sali, A. (1998) Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. USA 95(23), 13597-13602.
27. Shortle, D., Simons, K. T., and Baker, D. (1998) Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. USA 95(19), 11158-11162.
28. Simons, K. T., Bonneau, R., Ruczinski, I., and Baker, D. (1999a) Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl. 3, 171-176.
29. Simons, K. T., Kooperberg, C., Huang, E., and Baker, D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol. 268, 209-225.
30. Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C., and Baker, D. (1999b) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34(1), 82-95.
31. Simons, Kim T., Strauss, Charlie E. M., Baker, David. (2001) Prospects for ab initio protein structural genomics. J. Mol. Biol. 306, 1191-1199.
32. Sippl, M. J., Lackner, P., Domingues, F. S., and Koppensteiner, W. A. (1999) An attempt to analyse progress in fold recognition from CASP1 to CASP3. Proteins 37(S3), 226-230.
33. Venclovas, C., Zemla, A., Fidelis, K., and Moult, J. (1999) Some measures of comparative performance in the three CASPs. Proteins Suppl. 3, 231-237.
34. Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1996) Derivation of 3D coordinate templates for searching structural databases: Application to Ser-His-Asp catalytic triads in the serine proteinases and lipases. Protein Sci. 5(6), 1001-1013.