M-TASSER: An algorithm for protein quaternary structure prediction

Biophysical Journal

Volumn 94, Issue 3, 2008, Pages 918-928

  Chen, Huiling ^a   Skolnick, Jeffrey ^a  

^a GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; MONOMER;

ALGORITHM; ARTICLE; EXPERIMENTAL MODEL; INTERFACE PRESSURE; LABORATORY DIAGNOSIS; M TASSER; METHODOLOGY; PREDICTION; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN QUATERNARY STRUCTURE;

EID: 38549171298     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.107.114280     Document Type: Article

References (51)

1. von Mering, C., R. Krause, B. Snel, M. Cornell, S. G. Oliver, S. Fields, and P. Bork. 2002. Comparative assessment of large-scale data sets of protein-protein interactions. Nature. 417:399-403.
2. Kumar, A., and M. Snyder. 2002. Protein complexes take the bait. Nature. 415:123-124.
3. Rain, J., L. Selig, H. De Reuse, V. Battaglia, C. Reverdy, S. Simon, G. Lenzen, F. Petel, J. Wojcik, and V. Schachter. 2001. The protein-protein interaction map of Helicobacter pylori. Nature. 409:211-215.
4. Hazbun, T., and S. Fields. 2001. Networking proteins in yeast. Proc. Natl. Acad. Sci. USA. 98:4277-4278.
5. Uetz, P., L. Giot, G. Cagney, T. Mansfield, R. Judson, J. Knight, D. Lockshon, V. Narayan, M. Srinivasan, P. Pochart, A. Qureshi-Emili, Y. Li, et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature. 403:623-627.
6. Ito, T., T. Chiba, R. Osawa, M. Yoshida, M. Hattori, and Y. Sasaki. 2000. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA. 98:4569-4574.
7. Edwards, A. M., B. Kus, R. Jansen, D. Greenbaum, J. Greenblatt, and M. Gerstein. 2002. Bridging structural biology and genomics: assessing protein interaction data with known complexes. Trends Genet. 18:529-536.
8. Sali, A., R. Glaeser, T. Earnest, and W. Baumeister. 2003. From words to literature in structural proteomics. Nature. 422:216-225.
9. Russell, R. B., F. Alber, P. Aloy, F. P. Davis, D. Korkin, M. Pichaud, M. Topf, and A. Sali. 2004. A structural perspective on protein-protein interactions. Curr. Opin. Struct. Biol. 14:313-324.
10. Abbott, A. 2002. Proteomics: the society of proteins. Nature. 417:894-896.
11. Aloy, P., H. Ceulemans, A. Stark, and R. B. Russell. 2003. The relationship between sequence and interaction divergence in proteins. J. Mol. Biol. 332:989-998.
12. Aloy, P., M. Pichaud, and R. B. Russell. 2005. Protein complexes: structure prediction challenges for the 21st century. Curr. Opin. Struct. Biol. 15:15-22.
13. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
14. Szilagyi, A., V. Grimm, A. K. Arakaki, and J. Skolnick. 2005. Prediction of physical protein-protein interactions. Phys. Biol. 2:S1-S16.
15. Pieper, U., N. Eswar, H. Braberg, M. S. Madhusudhan, F. P. Davis, A. C. Stuart, N. Mirkovic, A. Rossi, M. A. Marti-Renom, A. Fiser, B. Webb, D. Greenblatt, et al. 2004. MODBASE, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 32:D217-D222.
16. Aloy, P., and R. B. Russell. 2003. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics. 19:161-162.
17. Aloy, P., and R. B. Russell. 2002. Interrogating protein interaction networks through structural biology. Proc. Natl. Acad. Sci. USA. 99:5896-5901.
18. Aloy, P., and R. B. Russell. 2004. Ten thousand interactions for the molecular biologist. Nat. Biotechnol. 22:1317-1321.
19. Apic, G., J. Gough, and S. A. Teichmann. 2001. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J. Mol. Biol. 310:311-325.
20. Sali, A. 2003. NIH workshop on structural proteomics of biological complexes. Structure. 11:1043-1047.
21. Lu, L., H. Lu, and J. Skolnick. 2002. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins. 49:350-364.
22. Lu, H., L. Lu, and J. Skolnick. 2003. Development of unified statistical potentials describing protein-protein interactions. Biophys. J. 84:1895-1901.
23. Lu, L., A. K. Arakaki, H. Lu, and J. Skolnick. 2003. Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome. Genome Res. 13:1146-1154.
24. Skolnick, J., D. Kihara, and Y. Zhang. 2004. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins. 56:502-518.
25. Grimm, V., Y. Zhang, and J. Skolnick. 2006. Benchmarking of dimeric threading and structure refinement. Proteins. 63:457-465.
26. Zhang, Y., and J. Skolnick. 2004. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc. Natl. Acad. Sci. USA. 101:7594-7599.
27. Zhang, Y., A. K. Arakaki, and J. Skolnick. 2005. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins. 61(Suppl. 7):91-98.
28. Zhang, Y., and J. Skolnick. 2004. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys. J. 87:2647-2655.
29. Zhang, Y., and J. Skolnick. 2004. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 25:865-871.
30. Wodak, S., and J. Janin. 1978. Computer analysis of protein-protein interactions. J. Mol. Biol. 124:323-342.
31. Dominguez, C., R. Boelens, and A. M. Bonvin. 2003. HADDOCK: a protein-protein docking approach based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125:1731-1737.
32. Janin, J., K. Henrick, J. Moult, L. Eyck, M. Sternberg, S. Vajda, I. Vakser, and S. Wodak. 2003. CAPRI: a critical assessment of predicted interactions. Proteins. 52:2-9.
33. Mendez, R., R. Leplae, M. F. Lensink, and S. J. Wodak. 2005. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins. 60:150-169.
34. Mendez, R., R. Leplae, L. De Maria, and S. J. Wodak. 2003. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins. 52:51-67.
35. Bonvin, A. M. 2006. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 16:194-200.
36. van Dijk, A. D., S. J. de Vries, C. Dominguez, H. Chen, H. X. Zhou, and A. M. Bonvin. 2005. Data-driven docking: HADDOCK's adventures in CAPRI. Proteins. 60:232-238.
37. Chen, H., and H. X. Zhou. 2005. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins. 61:21-35.
38. Zhang, Y., D. Kihara, and J. Skolnick. 2002. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins. 48:192-201.
39. Zhang, Y., A. Kolinski, and J. Skolnick. 2003. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys. J. 85:1145-1164.
40. Ponstingl, H., T. Kabir, and J. M. Thornton. 2003. Automatic inference of protein quaternary structure from crystals. J. Appl. Cryst. 36:1116-1122.
41. Henrick, K., and J. M. Thornton. 1998. PQS: a protein quaternary structure file server. Trends Biochem. Sci. 23:358-361.
42. Boeckmann, B., A. Bairoch, R. Apweiler, M. C. Blatter, A. Estreicher, E. Gasteiger, M. J. Martin, K. Michoud, C. O'Donovan, I. Phan, S. Pilbout, and M. Schneider. 2003. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:365-370.
43. Xu, Q., A. Canutescu, Z. Obradovic, and R. L. Dunbrack Jr. 2006. ProtBuD: a database of biological unit structures of protein families and superfamilies. Bioinformatics. 22:2876-2882.
44. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
45. Jones, D. 1999. Protein secondary structure prediction based on position-specific scoring matrics. J. Mol. Biol. 292:195-202.
46. Chen, H., and H. X. Zhou. 2005. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res. 33:3193-3199.
47. Zhou, H., and Y. Zhou. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11:2714-2726.
48. Zhang, C., S. Liu, H. Zhou, and Y. Zhou. 2003. An accurate, residue-level, pair potential of mean force for folding and binding based on the distance-scaled, ideal-gas reference state. Protein Sci. 13:400-411.
49. Zhang, Y., and J. Skolnick. 2005. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 33:2302-2309.
50. Zhang, Y., and J. Skolnick. 2004. Scoring function for automated assessment of protein structure template quality. Proteins. 57:702-710.
51. Reva, B. A., A. V. Finkelstein, and J. Skolnick. 1998. What is the probability of a chance prediction of a protein structure with an RMSD of 6 A? Fold. Des. 3:141-147.