Protein-protein complex structure predictions by multimeric threading and template recombination

Structure

Volumn 19, Issue 7, 2011, Pages 955-966

  Mukherjee, Srayanta ^a,c   Zhang, Yang ^a,b,c  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^c UNIVERSITY OF KANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MONOMER;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; COTH; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ALGORITHMS; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION MAPPING; PROTEIN MULTIMERIZATION; PROTEINS; SOFTWARE;

EID: 79960164372     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.04.006     Document Type: Article

References (49)

1. P. Aloy, and R.B. Russell Ten thousand interactions for the molecular biologist Nat. Biotechnol. 22 2004 1317 1321 (Pubitemid 39336787)
2. P. Aloy, B. Bottcher, H. Ceulemans, C. Leutwein, C. Mellwig, S. Fischer, A.C. Gavin, P. Bork, G. Superti-Furga, L. Serrano, and R.B. Russell Structure-based assembly of protein complexes in yeast Science 303 2004 2026 2029 (Pubitemid 38393279)
3. P. Aloy, M. Pichaud, and R.B. Russell Protein complexes: structure prediction challenges for the 21st century Curr. Opin. Struct. Biol. 15 2005 15 22 (Pubitemid 40249504)
4. S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Nucleic Acids Res. 25 1997 3389 3402 (Pubitemid 27359211)
5. R. Chen, L. Li, and Z. Weng ZDOCK: an initial-stage protein-docking algorithm Proteins 52 2003 80 87 (Pubitemid 36648854)
6. S.R. Comeau, D.W. Gatchell, S. Vajda, and C.J. Camacho ClusPro: a fully automated algorithm for protein-protein docking Nucleic Acids Res. 32 2004 W96 W99
7. D. Douguet, H.C. Chen, A. Tovchigrechko, and I.A. Vakser DOCKGROUND resource for studying protein-protein interfaces Bioinformatics 22 2006 2612 2618 (Pubitemid 44642599)
8. R. Finn, J. Mistry, B. Schuster-Bockler, S. Griffiths-Jones, V. Hollich, T. Lassmann, S. Moxon, M. Marshall, A. Khanna, and R. Durbin Pfam: clans, webtools and services Nucleic Acids Res. 34 2006 D247 D251
9. S. Fiorucci, and M. Zacharias Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT Proteins 78 2010 3131 3139
10. J.J. Gray, S. Moughon, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl, and D. Baker Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations J. Mol. Biol. 331 2003 281 299 (Pubitemid 36870793)
11. S.Y. Huang, and X. Zou MDockPP: a hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19 Proteins 78 2010 3096 3103
12. H. Hwang, B. Pierce, J. Mintseris, J. Janin, and Z. Weng Protein-protein docking benchmark version 3.0 Proteins 73 2008 705 709 (Pubitemid 352788651)
13. H. Hwang, T. Vreven, B.G. Pierce, J.H. Hung, and Z. Weng Performance of ZDOCK and ZRANK in CAPRI rounds 13-19 Proteins 78 2010 3104 3110
14. J. Janin The targets of CAPRI Rounds 13-19 Proteins 78 2010 3067 3072
15. D.T. Jones Protein secondary structure prediction based on position-specific scoring matrices J. Mol. Biol. 292 1999 195 202 (Pubitemid 29435759)
16. E. Katchalski-Katzir, I. Shariv, M. Eisenstein, A.A. Friesem, C. Aflalo, and I.A. Vakser Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. USA 89 1992 2195 2199
17. D. Kozakov, D.R. Hall, D. Beglov, R. Brenke, S.R. Comeau, Y. Shen, K. Li, J. Zheng, P. Vakili, I. Paschalidis, and S. Vajda Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19 Proteins 78 2010 3124 3130
18. A. Kryshtafovych, K. Fidelis, and J. Moult CASP8 results in context of previous experiments Proteins 77 Suppl 9 2009 217 228
19. P.J. Kundrotas, M.F. Lensink, and E. Alexov Homology based modelling of 3D structures of protein complexes using alignments of modified sequence profiles Int. J. Biol. Macromol. 43 2008 198 208
20. M. Lensink, and S. Wodak Docking and scoring protein interactions: CAPRI 2009 Proteins 78 2010 3073 3084
21. M.F. Lensink, and S.J. Wodak Blind predictions of protein interfaces by docking calculations in CAPRI Proteins 78 2010 3085 3095
22. L. Li, R. Chen, and Z. Weng RDOCK: refinement of rigid-body protein docking predictions Proteins 53 2003 693 707 (Pubitemid 37352182)
23. S. Lorenzen, and Y. Zhang Identification of near-native structures by clustering protein docking conformations Proteins 68 2007 187 194 (Pubitemid 46871592)
24. S. Lorenzen, and Y. Zhang Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization Protein Sci. 16 2007 2716 2725 (Pubitemid 350172758)
25. L. Lu, H. Lu, and J. Skolnick MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading Proteins 49 2002 350 364 (Pubitemid 35231471)
26. R. Mendez, R. Leplae, L. De Maria, and S.J. Wodak Assessment of blind predictions of protein-protein interactions: current status of docking methods Proteins 52 2003 51 67 (Pubitemid 36648851)
27. R. Mendez, R. Leplae, M.F. Lensink, and S.J. Wodak Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures Proteins 60 2005 150 169 (Pubitemid 40934881)
28. J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, and A. Tramontano Critical assessment of methods of protein structure prediction-Round VIII Proteins 77 2009 1 4
29. S. Mukherjee, and Y. Zhang MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming Nucleic Acids Res. 37 2009 e83
30. Y. Ofran, and B. Rost Predicted protein-protein interaction sites from local sequence information FEBS Lett. 544 2003 236 239 (Pubitemid 36628069)
31. R.B. Russell, F. Alber, P. Aloy, F.P. Davis, D. Korkin, M. Pichaud, M. Topf, and A. Sali A structural perspective on protein-protein interactions Curr. Opin. Struct. Biol. 14 2004 313 324 (Pubitemid 38749059)
32. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815 (Pubitemid 24007801)
33. K.T. Simons, C. Strauss, and D. Baker Prospects for ab initio protein structural genomics J. Mol. Biol. 306 2001 1191 1199 (Pubitemid 33030014)
34. A. Sircar, and J.J. Gray SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models PLoS Comput. Biol. 6 2010 e1000644
35. A. Sircar, S. Chaudhury, K.P. Kilambi, M. Berrondo, and J.J. Gray A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19 Proteins 78 2010 3115 3123
36. J. Skolnick, D. Kihara, and Y. Zhang Development and large scale benchmark testing of the PROSPECTOR 3.0 threading algorithm Proteins 56 2004 502 518 (Pubitemid 38924963)
37. A. Tovchigrechko, and I.A. Vakser Development and testing of an automated approach to protein docking Proteins 60 2005 296 301 (Pubitemid 40934902)
38. A. Tovchigrechko, and I.A. Vakser GRAMM-X public web server for protein-protein docking Nucleic Acids Res. 34 2006 W310 W314
39. S. Vajda, and C.J. Camacho Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol. 22 2004 110 116 (Pubitemid 38230388)
40. K. Wiehe, B. Pierce, W.W. Tong, H. Hwang, J. Mintseris, and Z. Weng The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI Proteins 69 2007 719 725 (Pubitemid 350210130)
41. S. Wu, and Y. Zhang LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res. 35 2007 3375 3382 (Pubitemid 47073600)
42. S. Wu, and Y. Zhang MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information Proteins 72 2008 547 556 (Pubitemid 351928511)
43. S. Wu, J. Skolnick, and Y. Zhang Ab initio modeling of small proteins by iterative TASSER simulations BMC Biol. 5 2007 17
44. M. Zacharias ATTRACT: protein-protein docking in CAPRI using a reduced protein model Proteins 60 2005 252 256 (Pubitemid 40934895)
45. Y. Zhang Progress and challenges in protein structure prediction Curr. Opin. Struct. Biol. 18 2008 342 348
46. Y. Zhang I-TASSER: fully automated protein structure prediction in CASP8 Proteins 77 2009 100 113
47. Y. Zhang, and J. Skolnick Automated structure prediction of weakly homologous proteins on a genomic scale Proc. Natl. Acad. Sci. USA 101 2004 7594 7599 (Pubitemid 38658074)
48. Y. Zhang, and J. Skolnick Scoring function for automated assessment of protein structure template quality Proteins 57 2004 702 710 (Pubitemid 39626992)
49. Y. Zhang, and J. Skolnick The protein structure prediction problem could be solved using the current PDB library Proc. Natl. Acad. Sci. USA 102 2005 1029 1034 (Pubitemid 40170720)