Improving consensus contact prediction via server correlation reduction

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Gao, Xin ^a,b   Xu, Jinbo ^c   Li, Ming ^a   Bu, Dongbo ^b  

^a UNIVERSITY OF WATERLOO   (Canada)

^b INSTITUTE OF COMPUTING TECHNOLOGY   (China)

^c TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; ASSAY; CONTROLLED STUDY; CORRELATION ANALYSIS; EVALUATION RESEARCH; EXPERIMENTAL MODEL; MUTATIONAL ANALYSIS; PRINCIPAL COMPONENT ANALYSIS; PROTEIN ANALYSIS; SCORING SYSTEM; AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONSENSUS SEQUENCE; METHODOLOGY; PROTEIN BINDING; SEQUENCE ANALYSIS; SYSTEM ANALYSIS;

PROTEIN;

AMINO ACID SEQUENCE; ARTIFICIAL INTELLIGENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; CONSENSUS SEQUENCE; MODELS, MOLECULAR; PROGRAMMING, LINEAR; PROTEIN BINDING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 67649535959     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-28     Document Type: Article

References (56)

1. Y Xu D Xu J Liang, Computational Methods for Protein Structure Prediction and Modeling New York: Springer 2007 1
2. Y Xu D Xu J Liang, Computational Methods for Protein Structure Prediction and Modeling New York: Springer 2007 2
3. Critical assessment of methods of protein structure prediction (CASP):Round V. J Moult K Fidelis A Zemla T Hubbard, Proteins. 2003 53 Suppl 6 334 339 14579322 (Pubitemid 37352192)
4. Critical assessment of methods of protein structure prediction (CASP):Round VI. J Moult K Fidelis B Rost T Hubbard A Tramontano, Proteins 2005 61 3 7 16187341 (Pubitemid 43069953)
5. CASP6 assessment of contact prediction. O Grana D Baker R MacCallum J Meiler M Punta B Rost M Tress A Valencia, Proteins 2005 61 214 224 16187364 (Pubitemid 43069976)
6. CASP7 presentation on contact prediction. N Clarke A Valencia J Izarzugaza M Tress O Grana, 2009 http://predictioncenter.org/casp7/meeting/ presentations/Presentations-assessors/CASP7-RR-Clarke.pdf
7. Critical assessment of methods of protein structure prediction (CASP):Round VII. J Moult K Fidelis A Kryshtafovych B Rost T Hubbard A Tramontano, Proteins 2007 69 3 9 17918729 (Pubitemid 350210108)
8. The Protein Data Bank. H Berman J Westbrook Z Feng G Gilliland T Bhat H Weissig I Shindyalov P Bourne, Nucleic Acids Res 2000 28 235 242 10592235 (Pubitemid 30047768)
9. Physically realistic homology models built with Rosetta can be more accurate than their templates. K Misura D Chivian C Rohl D Kim D Baker, Proc Natl Acad Sci U S A. 2006 103 14 5361 5366 16567638
10. Automated prediction of CASP-5 structures using the Robetta server. D Chivian DE Kim L Malmström P Bradley T Robertson P Murphy CE Strauss R Bonneau CA Rohl D Baker, Proteins 2003 53 Suppl 6 524 533 14579342 (Pubitemid 37352212)
11. Template-based modeling and free modeling by I-TASSER in CASP7. Y Zhang, Proteins 2007 69 Suppl 8 108 117 17894355 (Pubitemid 350210118)
12. TASSER: An automated method for the prediction of protein tertiary structures in CASP6. Y Zhang A Arakaki J Skolnick, Proteins 2005 61 Suppl 7 91 98 16187349 (Pubitemid 43069961)
13. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Y Zhang A Kolinski J Skolnick, Biophys J. 2003 85 2 1145 1164 12885659 (Pubitemid 36909676)
14. Estimation of effective interresidue contact energies from protein crystal-structures quasi-chemical approximation. S Miyazawa R Jernigan, Macromolecules 1985 18 534 552
15. Calculation of conformational ensembles from potentials of mean force. M Sippl, J Mol Biol. 1990 213 4 859 883 2359125
16. Neural Net Representations of Empirical Protein Potentials. T Grossman R Farber A Lapedes, Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology (ISMB) 1995 154 161
17. Recognizing native folds by the arrangement of hydrophobic and polar residues. E Huang S Subbiah M Levitt, J Mol Biol 1995 249 493 507 7783205
18. Correlated mutations and residue contacts in proteins. U Göbel C Sander R Schneider A Valencia, Proteins 1994 18 309 317 8208723 (Pubitemid 24111530)
19. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? I Shindyalov N Kolchanov C Sander, Protein Eng 1994 7 3 349 358 8177884 (Pubitemid 24063134)
20. Compensating changes in protein multiple sequence alignments. W Taylor K Hatrick, Protein Eng. 1994 7 3 341 348 8177883 (Pubitemid 24063133)
21. The prediction of protein contacts from multiple sequence alignments. D Thomas G Casari C Sander, Protein Eng 1996 9 11 941 948 8961347 (Pubitemid 26402297)
22. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. O Olmea A Valencia, Fold Des. 1997 2 3 S25 S32 9218963
23. Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families. I Halperin H Wolfson R Nussinov, Proteins 2006 63 832 845 16508975 (Pubitemid 43765137)
24. Predicting residue contacts using pragmatic correlated mutations method: reducing the false positives. P Kundrotas E Alexov, BMC Bioinformatics. 2006 7 503 511 17109752
25. Progress in predicting inter-residue contacts of proteins with neural networks and correlated mutations. P Fariselli O Olmea A Valencia R Casadio, Proteins 2001 5 157 162 11835493 (Pubitemid 34113179)
26. Prediction of contact maps with neural networks and correlated mutations. P Fariselli O Olmea A Valencia R Casadio, Protein Eng 2001 14 11 835 843 11742102 (Pubitemid 34024175)
27. Prediction of protein residue contacts with a PDB-derived likelihood matrix. M Singer G Vriend R Bywater, Protein Eng. 2002 15 9 721 725 12456870 (Pubitemid 35470428)
28. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. G Pollastri P Baldi, Bioinformatics 2002 18 S62 70 12169532
29. Prediction of contact maps using Support Vector Machines. Y Zhao G Karypis, Proceedings of the Third IEEE International Conference on Bioinformatics and Bioengineering (BIBE) 2003 26 33
30. Protein contact prediction using patterns of correlation. N Hamilton K Burrage M Ragan T Huber, Proteins 2004 56 679 684 15281121 (Pubitemid 39063311)
31. PROFcon: novel prediction of long-range contacts. M Punta B Rost, Bioinformatics 2005 21 2960 2968 15890748 (Pubitemid 40916420)
32. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. S Wu Y Zhang, Bioinformatics. 2008 24 7 924 931 18296462
33. Contact prediction using mutual information and neural nets. G Shackelford K Karplus, Proteins 2007 69 159 164 17932918 (Pubitemid 350210123)
34. Mining residue contacts in proteins using local structure predictions. M Zaki S Jin C Bystroff, IEEE Trans Syst Man Cybern B Cybern 2003 33 5 789 801 18238232
35. Predicting interresidue contacts using templates and pathways. Y Shao C Bystroff, Proteins 2003 53 497 502 14579339 (Pubitemid 37352209)
36. LOMETS: a local meta-threading-server for protein structure prediction. S Wu Y Zhang, Nucleic Acids Res 2007 35 3375 3382 17478507 (Pubitemid 47073600)
37. HMMSTR: A hidden Markov model for local sequence-structure correlations in proteins. C Bystroff V Thorsson D Baker, J Mol Biol. 2000 301 1 173 190 10926500 (Pubitemid 30701055)
38. FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J Shi T Blundell K Mizuguchi, J Mol Biol 2001 310 243 257 11419950 (Pubitemid 32619966)
39. Protein homology detection by HMM-HMM comparison. J Soding, Bioinformatics 2005 21 951 960 15531603 (Pubitemid 40467915)
40. A practical method for interpretation of threading scores: an application of neural networks. Y Xu D Xu V Olman, Statistica Sinica Special Issue on Bioinformatics 2002 12 159 177
41. Hidden Markov Models for detecting remote protein homologies. BCK Karplus R Hughey, Bioinformatics 1998 14 10 846 856 9927713 (Pubitemid 29041540)
42. Fold recognition by combining sequence profiles derived from evolution and from depth dependent structural alignment of fragments. H Zhou Y Zhou, Proteins. 2005 58 2 321 328 15523666 (Pubitemid 40076048)
43. Assessment of intramolecular contact predictions for CASP7. J Izarzugaza O Grana M Tress A Valencia N Clarke, Proteins 2007 69 152 158 17671976 (Pubitemid 350210122)
44. A machine learning information retrieval approach to protein fold recognition. J Cheng P Baldi, Bioinformatics 2006 22 1456 1463 16547073 (Pubitemid 43985316)
45. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. D Jones, J Mol Biol 1999 287 797 815 10191147 (Pubitemid 29176514)
46. Improvement of the GenTHREADER method for genomic fold recognition. L McGuffin D Jones, Bioinformatics 2003 19 874 881 12724298 (Pubitemid 36582404)
47. Protein threading by linear programming. J Xu M Li G Lin D Kim Y Xu, Pac Symp Biocomput 2003 264 275 12603034
48. Protein fold recognition by predicted alignment accuracy. J Xu, ACM/IEEE Trans Comput Biol Bioinform 2005 2 2 157 165 (Pubitemid 41049916)
49. A fast program for clustering and comparing large sets of protein or nucleotide sequences. W Li A Godzik, Bioinformatics 2006 22 1658 1659 16731699 (Pubitemid 43985301)
50. The zinc finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast. V Heurgue-Hamard M Graille N Scrima N Ulryck S Champ H van Tilbeurgh R Buckingham, J Biol Chem 2006 281 36140 36148 17008308 (Pubitemid 46041348)
51. Solution NMR Structure of Bacillus subtilis Hypothetical Protein yvyC. A Eletsky G Liu H Atreya D Sukumaran D Wang K Cunningham H Janjua LC Ma R Xiao J Liu M Baran T Acton B Rost G Montelione T Szyperski, 2007 http://www.pdb.org/ pdb/explore.do?structureId=2HC5
52. Scoring function for automated assessment of protein structure template quality. Y Zhang J Skolnick, Proteins 2004 57 702 710 15476259 (Pubitemid 39626992)
53. Prediction of CASP6 structures using automated Robetta protocols. D Chivian D Kim L Malmström J Schonbrun C Rohl D Baker, Proteins 2005 61 Suppl 7 57 66
54. Contact prediction in protein modeling: scoring, folding and refinement of coarse-grained models. D Latek A Kolinski, BMC Struct Biol 2008 8 36 50 18694501
55. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. S Altschul T Madden A Schäffer J Zhang Z Zhang W Miller D Lipman, Nucleic Acids Res 1997 25 3389 3402 9254694 (Pubitemid 27359211)
56. Protein secondary structure prediction based on position-specific scoring matrices. D Jones, J Mol Biol. 1999 292 2 195 202 10493868 (Pubitemid 29435759)