Alternating evolutionary pressure in a genetic algorithm facilitates protein model selection

BMC Structural Biology

Volumn 8, Issue , 2008, Pages

  Offman, Marc N ^a   Tournier, Alexander L ^a   Bates, Paul A ^a  

^a THE FRANCIS CRICK INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; EVOLUTIONARY ALGORITHM; GENETIC ALGORITHM; MATHEMATICAL ANALYSIS; NUCLEAR MAGNETIC RESONANCE; PROTEIN ANALYSIS; PROTEIN MODIFICATION; PROTEIN STRUCTURE; ALGORITHM; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETIC RECOMBINATION; GENETICS; MOLECULAR EVOLUTION; PROTEIN DATABASE; SEQUENCE ALIGNMENT; THERMODYNAMICS;

PROTEIN;

ALGORITHMS; COMPUTER SIMULATION; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; MODELS, GENETIC; MODELS, MOLECULAR; PROTEINS; RECOMBINATION, GENETIC; SEQUENCE ALIGNMENT; SOFTWARE DESIGN; THERMODYNAMICS;

EID: 50849118769     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-34     Document Type: Article

References (64)

1. Progress from CASP6 to CASP7. A Kryshtafovych K Fidelis J Moult, Proteins 2007 69 Suppl 8 194 207 17918728
2. Progress over the first decade of CASP experiments. A Kryshtafovych C Venclovas K Fidelis J Moult, Proteins 2005/09/28 2005 61 Suppl 7 225 236 16187365
3. Evaluating the usefulness of protein structure models for molecular replacement. A Giorgetti D Raimondo AE Miele A Tramontano, Bioinformatics 2005/10/06 2005 21 Suppl 2 ii72 6 16204129
4. The importance of alignment accuracy for molecular replacement. R Schwarzenbacher A Godzik SK Grzechnik L Jaroszewski, Acta Crystallogr D Biol Crystallogr 2004/06/24 2004 60 Pt 7 1229 1236 15213384
5. Molecular Replacement techniques in the context of structural genomics. M Delarue, Practical Approaches Series Eds. Oxford University Press., Sanderson MR, Skelly J, 2005
6. Structural genomics and its importance for gene function analysis. J Skolnick JS Fetrow A Kolinski, Nat Biotechnol 2000/03/04 2000 18 3 283 287 10700142
7. Novel technologies for virtual screening. T Lengauer C Lemmen M Rarey M Zimmermann, Drug Discov Today 2004/02/06 2004 9 1 27 34 14761803
8. Automated server predictions in CASP7. JN Battey J Kopp L Bordoli RJ Read ND Clarke T Schwede, Proteins 2007/09/27 2007 69 Suppl 8 68 82 17894354
9. Assessment of CASP7 predictions for template-based modeling targets. J Kopp L Bordoli JN Battey F Kiefer T Schwede, Proteins 2007/09/27 2007 69 Suppl 8 38 56 17894352
10. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. WR Pearson, Genomics 1991/11/01 1991 11 3 635 650 1774068
11. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990/10/05 1990 215 3 403 410 2231712
12. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997/09/01 1997 25 17 3389 3402 9254694
13. Profile hidden Markov models. SR Eddy, Bioinformatics 1999/01/27 1998 14 9 755 763 9918945
14. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. R Sadreyev N Grishin, J Mol Biol 2003/01/28 2003 326 1 317 336 12547212
15. The HHpred interactive server for protein homology detection and structure prediction. J Soding A Biegert AN Lupas, Nucleic Acids Res 2005/06/28 2005 33 Web Server issue W244 8 15980461
16. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. G Yona M Levitt, J Mol Biol 2002/02/06 2002 315 5 1257 1275 11827492
17. FFAS03: a server for profile - profile sequence alignments. L Jaroszewski L Rychlewski Z Li W Li A Godzik, Nucleic Acids Res 2005/06/28 2005 33 Web Server issue W284 8 15980471
18. Critical assessment of methods of protein structure prediction-Round VII. J Moult K Fidelis A Kryshtafovych B Rost T Hubbard A Tramontano, Proteins 2007/10/09 2007 69 Suppl 8 3 9 17918729
19. Assessment of CASP7 predictions in the high accuracy template-based modeling category. RJ Read G Chavali, Proteins 2007/09/27 2007 69 Suppl 8 27 37 17894351
20. Comparative protein modelling by satisfaction of spatial restraints. A Sali TL Blundell, J Mol Biol 1993/12/05 1993 234 3 779 815 8254673
21. In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. B Contreras-Moreira PW Fitzjohn PA Bates, J Mol Biol 2003/04/23 2003 328 3 593 608 12706719
22. Developing a move-set for protein model refinement. MN Offman PW Fitzjohn PA Bates, Bioinformatics 2006/05/18 2006 22 15 1838 1845 16705011
23. Modelling zinc-binding proteins with GADGET: genetic algorithm and distance geometry for exploring topology. K Petersen WR Taylor, J Mol Biol 2003/01/16 2003 325 5 1039 1059 12527307
24. Improved genetic algorithm for the protein folding problem by use of a Cartesian combination operator. AA Rabow HA Scheraga, Protein Sci 1996/09/01 1996 5 9 1800 1815 8880904
25. Protein refolding in silico with atom-based statistical potentials and conformational search using a simple genetic algorithm. Q Fang D Shortle, J Mol Biol 2006/05/09 2006 359 5 1456 1467 16678202
26. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. R Das B Qian S Raman R Vernon J Thompson P Bradley S Khare MD Tyka D Bhat D Chivian DE Kim WH Sheffler L Malmstrom AM Wollacott C Wang I Andre D Baker, Proteins 2007/09/27 2007 69 Suppl 8 118 128 17894356
27. Molecular dynamics in the endgame of protein structure prediction. MR Lee J Tsai D Baker PA Kollman, J Mol Biol 2002/01/22 2001 313 2 417 430 11800566
28. Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. B Qian AR Ortiz D Baker, Proc Natl Acad Sci U S A 2004/10/20 2004 101 43 15346 15351 15492216
29. I-TASSER server for protein 3D structure prediction. Y Zhang, BMC Bioinformatics 2008/01/25 2008 9 1 40 18215316
30. Analysis of TASSER-based CASP7 protein structure prediction results. H Zhou SB Pandit SY Lee J Borreguero H Chen L Wroblewska J Skolnick, Proteins 2007/08/21 2007 69 Suppl 8 90 97 17705276
31. Fams-ace: a combined method to select the best model after remodeling all server models. G Terashi M Takeda-Shitaka K Kanou M Iwadate D Takaya A Hosoi K Ohta H Umeyama, Proteins 2007/09/27 2007 69 Suppl 8 98 107 17894329
32. High accuracy template based modeling by global optimization. K Joo J Lee S Lee JH Seo SJ Lee, Proteins 2007/09/27 2007 69 Suppl 8 83 89 17894332
33. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. A Kolinski JM Bujnicki, Proteins 2005/09/28 2005 61 Suppl 7 84 90 16187348
34. Servers for protein structure prediction. D Fischer, Curr Opin Struct Biol 2006/03/21 2006 16 2 178 182 16546376
35. Assessment of predictions in the model quality assessment category. D Cozzetto A Kryshtafovych M Ceriani A Tramontano, Proteins 2007/08/08 2007 69 Suppl 8 175 183 17680695
36. Solvation energy in protein folding and binding. D Eisenberg AD McLachlan, Nature 1986/01/16 1986 319 6050 199 203 3945310
37. VERIFY3D: assessment of protein models with three-dimensional profiles. D Eisenberg R Luthy JU Bowie, Methods Enzymol 1997/01/01 1997 277 396 404 9379925
38. Benchmarking consensus model quality assessment for protein fold recognition. LJ McGuffin, BMC Bioinformatics 2007/09/20 2007 8 345 17877795
39. Improving sequence-based fold recognition by using 3D model quality assessment. CS Pettitt LJ McGuffin DT Jones, Bioinformatics 2005/06/16 2005 21 17 3509 3515 15955780
40. Recognition of errors in three-dimensional structures of proteins. MJ Sippl, Proteins 1993/12/01 1993 17 4 355 362 8108378
41. The victor/FRST function for model quality estimation. SC Tosatto, J Comput Biol 2005/12/29 2005 12 10 1316 1327 16379537
42. Can correct protein models be identified? B Wallner A Elofsson, Protein Sci 2003/04/30 2003 12 5 1073 1086 12717029
43. Seventh Meeting on the Critical Assessment of Techniques for Protein Structure Prediction. TL Trapane EE Lattman, Proteins 2007 69 Suppl 8 1 2 17957767
44. Protein Structure Prediction Center webpage. CASP, http://www. predictioncenter.org/
45. Protein secondary structure prediction based on position-specific scoring matrices. DT Jones, J Mol Biol 1999/09/24 1999 292 2 195 202 10493868
46. Conformation of polypeptides and proteins. GN Ramachandran V Sasisekharan, Adv Protein Chem 1968/01/01 1968 23 283 438 4882249
47. Cyclic coordinate descent: A robotics algorithm for protein loop closure. AA Canutescu RL Dunbrack Jr., Protein Sci 2003/04/30 2003 12 5 963 972 12717019
48. Scoring function for automated assessment of protein structure template quality. Y Zhang J Skolnick, Proteins 2004/10/12 2004 57 4 702 710 15476259
49. Processing and analysis of CASP3 protein structure predictions. A Zemla C Venclovas J Moult K Fidelis, Proteins 1999/10/20 1999 Suppl 3 22 29 10526349
50. MaxSub: an automated measure for the assessment of protein structure prediction quality. N Siew A Elofsson L Rychlewski D Fischer, Bioinformatics 2000/12/08 2000 16 9 776 785 11108700
51. A simplex method for function minimization. R Mead JA Nelder, Comp J 1965 7 308 313
52. Knowledge-based protein secondary structure assignment. D Frishman P Argos, Proteins 1995/12/01 1995 23 4 566 579 8749853
53. A graph-theory algorithm for rapid protein side-chain prediction. AA Canutescu AA Shelenkov RL Dunbrack Jr., Protein Sci 2003/08/22 2003 12 9 2001 2014 12930999
54. Effective energy functions for protein structure prediction. T Lazaridis M Karplus, Curr Opin Struct Biol 2000/04/08 2000 10 2 139 145 10753811
55. POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level. L Cavallo J Kleinjung F Fraternali, Nucleic Acids Res 2003/06/26 2003 31 13 3364 3366 12824328
56. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. C Zhang S Liu Y Zhou, Protein Sci 2004/01/24 2004 13 2 391 399 14739324
57. CHARMM: A program for macromolecular energy, minimization, and dynamics calculation. B Brooks R Bruccoleri B Olafson D States S Swaminathan M Karplus, J Comp Chem 1983 4 187 217
58. 3D Jigsaw 3.0 Modelling Server powered by POPULUS. MN Offman, http://bmm.cancerresearchuk.org/∼populus
59. Comparative protein structure modeling using MODELLER. N Eswar B Webb MA Marti-Renom MS Madhusudhan D Eramian MY Shen U Pieper A Sali, Curr Protoc Protein Sci 2008/04/23 2007 Chapter 2 Unit 2 9 18429317
60. Genetic algorithms: principles of natural selection applied to computation. S Forrest, Science 1993/08/13 1993 261 5123 872 878 8346439
61. High-resolution structure prediction and the crystallographic phase problem. B Qian S Raman R Das P Bradley AJ McCoy RJ Read D Baker, Nature 2007/10/16 2007 450 7167 259 264 17934447
62. Finite population models of dynamic optimization with stochastically alternating fitness functions. AML Liekens HMM ten Eikelder PAJ Hilbers, In IEEE Conf Evolutionary Computation 2003 2 838 845
63. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. M Wiederstein MJ Sippl, Nucleic Acids Res 2007/05/23 2007 35 Web Server issue W407 10 17517781
64. PROCHECK: a program to check the stereochemical quality of protein structures. LR Laskowski, J Appl Cryst 1993 26 283 291