Atomic-level protein structure refinement using fragment-guided molecular dynamics conformation sampling

Structure

Volumn 19, Issue 12, 2011, Pages 1784-1795

  Zhang, Jian ^a   Liang, Yu ^b   Zhang, Yang ^a,c  

^a UNIVERSITY OF MICHIGAN   (United States)

^b CENTRAL STATE UNIVERSITY   (United States)

^c UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONFORMATION; FRAGMENTATION REACTION; MOLECULAR DYNAMICS; PHYSICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; QUALITY CONTROL; STIMULATION;

COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS;

EID: 82955239912     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2011.09.022     Document Type: Article

References (35)

1. B.J. Alder, and T.E. Wainwright Phase transition for a hard sphere system J. Chem. Phys. 27 1957 1208 1209
2. A.K. Arakaki, Y. Zhang, and J. Skolnick Large-scale assessment of the utility of low-resolution protein structures for biochemical function assignment Bioinformatics 20 2004 1087 1096 (Pubitemid 38660346)
3. J. Chen, and C.L. Brooks 3rd Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 67 2007 922 930 (Pubitemid 46753939)
4. V.B. Chen, W.B. Arendall 3rd, J.J. Headd, D.A. Keedy, R.M. Immormino, G.J. Kapral, L.W. Murray, J.S. Richardson, and D.C. Richardson MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D Biol. Crystallogr. 66 2010 12 21
5. J. Cheng A multi-template combination algorithm for protein comparative modeling BMC Struct. Biol. 8 2008 18
6. W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
7. D. Cozzetto, A. Kryshtafovych, K. Fidelis, J. Moult, B. Rost, and A. Tramontano Evaluation of template-based models in CASP8 with standard measures Proteins 77 Suppl 9 2009 18 28
8. H. Fan, and A.E. Mark Refinement of homology-based protein structures by molecular dynamics simulation techniques Protein Sci. 13 2004 211 220 (Pubitemid 38021155)
9. D. Fischer 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor Proteins 51 2003 434 441 (Pubitemid 36528828)
10. C.A. Floudas Computational methods in protein structure prediction Biotechnol. Bioeng. 97 2007 207 213 (Pubitemid 46852917)
11. K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski 3D-Jury: a simple approach to improve protein structure predictions Bioinformatics 19 2003 1015 1018 (Pubitemid 36675823)
12. D.A. Keedy, C.J. Williams, J.J. Headd, W.B. Arendall 3rd, V.B. Chen, G.J. Kapral, R.A. Gillespie, J.N. Block, A. Zemla, D.C. Richardson, and J.S. Richardson The other 90% of the protein: assessment beyond the Calphas for CASP8 template-based and high-accuracy models Proteins 77 Suppl 9 2009 29 49
13. J. Kopp, L. Bordoli, J.N. Battey, F. Kiefer, and T. Schwede Assessment of CASP7 predictions for template-based modeling targets Proteins 69 Suppl 8 2007 38 56 (Pubitemid 350210112)
14. M.R. Lee, J. Tsai, D. Baker, and P.A. Kollman Molecular dynamics in the endgame of protein structure prediction J. Mol. Biol. 313 2001 417 430 (Pubitemid 33587197)
15. J.L. MacCallum, L. Hua, M.J. Schnieders, V.S. Pande, M.P. Jacobson, and K.A. Dill Assessment of the protein-structure refinement category in CASP8 Proteins 77 Suppl 9 2009 66 80
16. I.K. McDonald, and J.M. Thornton Satisfying hydrogen bonding potential in proteins J. Mol. Biol. 238 1994 777 793 (Pubitemid 24168633)
17. S. Plimpton Fast parallel algorithms for short-range molecular-dynamics J. Comp. Physiol. 117 1995 1 19
18. S. Raman, R. Vernon, J. Thompson, M. Tyka, R. Sadreyev, J. Pei, D. Kim, E. Kellogg, F. DiMaio, and O. Lange Structure prediction for CASP8 with all-atom refinement using Rosetta Proteins 77 Suppl 9 2009 89 99
19. A. Roy, A. Kucukural, and Y. Zhang I-TASSER: a unified platform for automated protein structure and function prediction Nat. Protoc. 5 2010 725 738
20. A. Sali, and T.L. Blundell Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 234 1993 779 815 (Pubitemid 24007801)
21. C.M. Summa, and M. Levitt Near-native structure refinement using in vacuo energy minimization Proc. Natl. Acad. Sci. USA 104 2007 3177 3182 (Pubitemid 46364133)
22. A. Tramontano, and V. Morea Assessment of homology-based predictions in CASP5 Proteins 53 Suppl 6 2003 352 368 (Pubitemid 37352194)
23. G. Wang, and R.L. Dunbrack Jr. PISCES: a protein sequence culling server Bioinformatics 19 2003 1589 1591 (Pubitemid 37038881)
24. J.M. Wang, P. Cieplak, and P.A. Kollman How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21 2000 1049 1074
25. L. Wroblewska, A. Jagielska, and J. Skolnick Development of a physics-based force field for the scoring and refinement of protein models Biophys. J. 94 2008 3227 3240
26. S.T. Wu, and Y. Zhang LOMETS: a local meta-threading-server for protein structure prediction Nucleic Acids Res. 35 2007 3375 3382 (Pubitemid 47073600)
27. J. Xu, and Y. Zhang How significant is a protein structure similarity with TM-score = 0.5? Bioinformatics 26 2010 889 895
28. A. Zemla LGA: A method for finding 3D similarities in protein structures Nucleic Acids Res. 31 2003 3370 3374 (Pubitemid 37442162)
29. J. Zhang, Q. Wang, B. Barz, Z. He, I. Kosztin, Y. Shang, and D. Xu MUFOLD: A new solution for protein 3D structure prediction Proteins 78 2010 1137 1152
30. Y. Zhang Template-based modeling and free modeling by I-TASSER in CASP7 Proteins 69 Suppl 8 2007 108 117 (Pubitemid 350210118)
31. Y. Zhang I-TASSER: fully automated protein structure prediction in CASP8 Proteins 77 Suppl 9 2009 100 113
32. Y. Zhang Protein structure prediction: when is it useful? Curr. Opin. Struct. Biol. 19 2009 145 155
33. Y. Zhang, and J. Skolnick Scoring function for automated assessment of protein structure template quality Proteins 57 2004 702 710 (Pubitemid 39626992)
34. Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309 (Pubitemid 41439897)
35. J. Zhu, H. Fan, X. Periole, B. Honig, and A.E. Mark Refining homology models by combining replica-exchange molecular dynamics and statistical potentials Proteins 72 2008 1171 1188