A study and benchmark of DNcon: A method for protein residue-residue contact prediction using deep networks

BMC Bioinformatics

Volumn 14, Issue SUPPL.14, 2013, Pages

  Eickholt, Jesse ^a   Cheng, Jianlin ^b,c  

^a CENTRAL MICHIGAN UNIVERSITY   (United States)

^b University of Missouri   (United States)

^c UNIVERSITY OF MISSOURI   (United States)

Author keywords

contact prediction; deep learning; deep networks; protein residue residue contact

Indexed keywords

ASSESSMENT TECHNIQUE; CRITICAL ASSESSMENT OF PROTEIN STRUCTURE PREDICTIONS (CASP); DEEP LEARNING; EVALUATION METRICS; LONG RANGE CONTACTS; MODEL QUALITY ASSESSMENTS; PROTEIN TERTIARY STRUCTURE PREDICTION; STANDARD EVALUATIONS;

FORECASTING; WEB SERVICES;

QUALITY CONTROL;

PROTEIN;

BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; PROCEDURES; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; ARTICLE; METHODOLOGY;

COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 84885355205     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S14-S12     Document Type: Article

References (28)

1. Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994, 18:309-317. 10.1002/prot.340180402, 8208723.
2. Kliger Y, Levy O, Oren A, Ashkenazy H, Tiran Z, Novik A, Rosenberg A, Amir A, Wool A, Toporik A, et al. Peptides modulating conformational changes in secreted chaperones: from in silico design to preclinical proof of concept. Proc Natl Acad Sci USA 2009, 106:13797-13801. 10.1073/pnas.0906514106, 2728974, 19666568.
3. Tress ML, Valencia A. Predicted residue-residue contacts can help the scoring of 3D models. Proteins 2010, 78:1980-1991.
4. Eickholt J, Wang Z, Cheng J. A conformation ensemble approach to protein residue-residue contact. BMC Struct Biol 2011, 11:38. 10.1186/1472-6807-11-38, 3200154, 21989082.
5. Wu S, Szilagyi A, Zhang Y. Improving protein structure prediction using multiple sequence-based contact predictions. Structure 2011, 19:1182-1191. 10.1016/j.str.2011.05.004, 3154634, 21827953.
6. Monastyrskyy B, Fidelis K, Tramontano A, Kryshtafovych A. Evaluation of residue-residue contact predictions in CASP9. Proteins 2011, 79(Suppl 10):119-125. 3226919, 21928322.
7. Ezkurdia I, Grana O, Izarzugaza JM, Tress ML. Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins 2009, 77(Suppl 9):196-209.
8. Duarte JM, Sathyapriya R, Stehr H, Filippis I, Lappe M. Optimal contact definition for reconstruction of contact maps. BMC Bioinformatics 2010, 11:283. 10.1186/1471-2105-11-283, 3583236, 20507547.
9. Tegge AN, Wang Z, Eickholt J, Cheng J. NNcon: improved protein contact map prediction using 2D-recursive neural networks. Nucleic Acids Res 2009, 37:W515-518. 10.1093/nar/gkp305, 2703959, 19420062.
10. Pollastri G, Baldi P. Prediction of contact maps by GIOHMMs and recurrent neural networks using lateral propagation from all four cardinal corners. Bioinformatics 2002, 18(Suppl 1):S62-70. 10.1093/bioinformatics/18.suppl_1.S62, 12169532.
11. Walsh I, Bau D, Martin AJ, Mooney C, Vullo A, Pollastri G. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks. BMC Struct Biol 2009, 9:5. 10.1186/1472-6807-9-5, 2654788, 19183478.
12. Fariselli P, Olmea O, Valencia A, Casadio R. Prediction of contact maps with neural networks and correlated mutations. Protein Eng 2001, 14:835-843. 10.1093/protein/14.11.835, 11742102.
13. Hamilton N, Burrage K, Ragan MA, Huber T. Protein contact prediction using patterns of correlation. Proteins 2004, 56:679-684. 10.1002/prot.20160, 15281121.
14. Cheng J, Baldi P. Improved residue contact prediction using support vector machines and a large feature set. BMC Bioinformatics 2007, 8:113. 10.1186/1471-2105-8-113, 1852326, 17407573.
15. Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008, 24:924-931. 10.1093/bioinformatics/btn069, 2648832, 18296462.
16. Di Lena P, Nagata K, Baldi P. Deep architectures for protein contact map prediction. Bioinformatics 2012, 28:2449-2457. 10.1093/bioinformatics/bts475, 22847931.
17. Eickholt J, Cheng J. Predicting protein residue-residue contacts using deep networks and boosting. Bioinformatics 2012, 28:3066-3072. 10.1093/bioinformatics/bts598, 23047561.
18. Li Y, Fang Y, Fang J. Predicting residue-residue contacts using random forest models. Bioinformatics 2011, 27:3379-3384. 10.1093/bioinformatics/btr579, 22016406.
19. Vicatos S, Reddy BV, Kaznessis Y. Prediction of distant residue contacts with the use of evolutionary information. Proteins 2005, 58:935-949. 10.1002/prot.20370, 15645442.
20. Olmea O, Valencia A. Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des 1997, 2:S25-32.
21. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. Protein 3D structure computed from evolutionary sequence variation. PLoS One 2011, 6:e28766. 10.1371/journal.pone.0028766, 3233603, 22163331.
22. Jones DT, Buchan DW, Cozzetto D, Pontil M. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. Bioinformatics 2012, 28:184-190. 10.1093/bioinformatics/btr638, 22101153.
23. CASP10. , http://www.predictioncenter.org/casp10/
24. Atchley WR, Zhao J, Fernandes AD, Druke T. Solving the protein sequence metric problem. Proc Natl Acad Sci USA 2005, 102:6395-6400. 10.1073/pnas.0408677102, 1088356, 15851683.
25. Cheng J, Randall AZ, Sweredoski MJ, Baldi P. SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 2005, 33:W72-76. 10.1093/nar/gki396, 1160157, 15980571.
26. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
27. CASP9. , http://www.predictioncenter.org/casp9/
28. Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999, 292:195-202. 10.1006/jmbi.1999.3091, 10493868.