Benchmarking of dimeric threading and structure refinement

Proteins: Structure, Function and Genetics

Volumn 63, Issue 3, 2006, Pages 457-465

  Grimm, Vera ^a   Zhang, Yang ^a   Skolnick, Jeffrey ^a,b  

^a UNIVERSITY AT BUFFALO   (United States)

^b GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Dimer model; Multimeric threading; Protein protein interactions; TASSER; Template quality

Indexed keywords

DIMER;

ALGORITHM; ANALYTIC METHOD; ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUALITY CONTROL; QUANTITATIVE ANALYSIS; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TASSER ALGORITHM;

ALGORITHMS; DATABASES, PROTEIN; DIMERIZATION; MODELS, STRUCTURAL; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, SECONDARY; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 33646033173     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.20878     Document Type: Article

References (31)

1. Lu L, Lu H, Skolnick J. MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 2002;49(3):350-364.
2. Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
3. von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 2002;417:399-403.
4. Aloy P, Russell RB. Ten thousand interactions for the molecular biologist. Nat Biotechnol 2004;22:1317-1321.
5. Kihara D, Skolnick J. The PDB is a covering set of small protein structures. J Mol Biol 2003;334:793-802.
6. Zhang Y, Skolnick J. The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci USA 2005;102:1029-1034.
7. Janin J. Assessing predictions of protein-protein interaction: the CAPRI experiment. Protein Sci 2005;14:278-283.
8. Szilágyi A, Grimm V, Arakaki A, Skolnick J. Prediction of physical protein-protein interactions. Phys Biol 2005:1-6.
9. Russell RB, Alber F, Aloy P, Davis FP, Korkin D, Pichaud M, Topf M, Sali A. A structural perspective on protein-protein interactions. Curr Opin Struct Biol 2004;14:313-324.
10. Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. Detecting protein function and protein-protein interactions from genome sequences. Science 1999;285:751-753.
11. Aloy P, Russell RB. Interrogating protein interaction networks through structural biology. Proc Natl Acad Sci USA 2002;99:5896-5901.
12. Aloy P, Russell RB. InterPreTS: protein interaction prediction through tertiary structure. Bioinformatics 2003;19:161-162.
13. Aloy P, Ceulemans H, Stark A, Russell RB. The relationship between sequence and interaction divergence in proteins. J Mol Biol 2003;332:989-998.
14. Pieper U, Eswar N, Stuart AC, Ilyin VA, Sali A. MODBASE, a database of annotated comparative protein structure models. Nucleic Acids Res 2002;30:255-259.
15. Yu H, Luscombe NM, Lu HX, Zhu X, Xia Y, Han JD, Bertin N, Chung S, Vidal M, Gerstein M. Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res 2004;14:1107-1118.
16. 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.
17. Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000;29:291-325.
18. Skolnick J, Kihara D, Zhang Y. Development and large scale benchmark testing of the PROSPECTOR_3 threading algorithm. Proteins 2004;56:502-518.
19. Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, Fagan P, Marvin J, Padilla D, Ravichandran V, Schneider B, Thanki N, Weissig H, Westbrook JD, Zardecki C. The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 2002;58:899-907.
20. Zhang L, Skolnick J. What should the Z-score of native protein structures be? Protein Sci 1998;7:1201-1207.
21. Zhang Y, Skolnick J. Tertiary structure predictions on a comprehensive benchmark of medium to large size proteins. Biophys J 2004;87:2647-2655.
22. Zhang Y, Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J Comput Chem 2004;25:865-871.
23. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci 1998;23:358-361.
24. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
25. Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 2005;33:2302-2309.
26. Sigrist CJ, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform 2002;3:265-274.
27. Betancourt MR, Skolnick J. Universal similarity measure for comparing protein structures. Biopolymers 2001;59:305-309.
28. Park SY, Beel BD, Simon MI, Bilwes AM, Crane BR. In different organisms, the mode of interaction between two signaling proteins is not necessarily conserved. Proc Natl Acad Sci USA 2004;101:11646-11651.
29. Ponstingl H, Kabir T, Gorse D, Thornton JM. Morphological aspects of oligomeric protein structures. Prog Biophys Mol Biol 2005;89:9-35.
30. Bandyopadhyay S, Cookson MR. Evolutionary and functional relationships within the DJ1 superfamily. BMC Evol Biol 2004;4:6.
31. Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000;41:47-57.