Efficlent identification of near-native conformations in ab initio protein structure prediction using structural profiles

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 2, 2010, Pages 249-258

  Wolff, Katrin ^a   Vendruscolo, Michele ^b   Porto, Markus ^a  

^a DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Artificial neural network; Critical assessment of structure prediction (casp); Position specific scoring matrices (pssms); Protein structural profiles; Protein structure prediction

Indexed keywords

AB INITIO CALCULATION; ACCURACY; AMINO ACID SEQUENCE; ARTICLE; ENERGY; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE; ARTIFICIAL NEURAL NETWORK; BIOLOGY; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; PROTEIN FOLDING;

PROTEIN;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; NEURAL NETWORKS (COMPUTER); PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS;

EID: 77449159842     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22533     Document Type: Article

References (28)

1. Kryshtafovych A, Venclovas C, Fidelis K, Moult J. Progress over the first decade of CASP experiments. Proteins 2005;61:225-236.
2. Kolinski A, Bujnicki JM. Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 2005;61:84-90.
3. Bradley P, Misura KMS, Baker D. Toward, high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
4. Kryshtafovych A, Fidelia K, Moult J. Progress from CASP6 to CASP7. Proteins 2007;69:194-207.
5. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007;69:108-117.
6. Kopp J, Bordoli L, Battey JN, Kiefer F, Schwede T. Assessment of CASP7 predictions for template-based modeling targets. Proteins 2007;69:38-56.
7. Jauch R, Yeo HC, Kolatkar PR, Clarke ND. Assessment of CAS.P7 structure predictions for template free targets. Proteins 2007;69:57-67.
8. Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004;383:66.
9. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
10. Simons K, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions. J Mol Biol 1997;268:209-225.
11. Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Annu Rev Biophys Biomol Struct 2001;30: 173-189. (Pubitemid 32566161)
12. Betancourt MR, Skolnick J. Finding the needle in a haystack: educing native folds from ambiguous ab initio protein structure predictions. J Comput Chem 2001;22:339-353.
13. Gong H, Fleming PJ, Rose GD. Building native protein, conformation from highly approximate backbone torsion angles. Proc Natl Acad Sci USA 2005;102:16227-16232.
14. Qiu J, Sheffler W, Baker D, Noble WS. Ranking predicted protein structures with support, vector regression. Proteins 2008:71:1175-1182.
15. Stumpff-Kane AW, Feig M. A correlation-based method for the enhancement of scoring functions on. funnel-shaped energy landscapes. Proteins 2006;63:155-164.
16. Cavalli A, Salvatella X, Dobson CM, Vendruscolo M. Protein structure determination from NMR chemical shifts. Proc Natl Acad Sci USA 2007;104:9615-9620.
17. Shen Y, Lange O, Delaglio F, Rossi P, Aramini JM, Liu G, Eletsky A, Wu Y, Singarapu KK, Lemak A, Ignatchenko A, Arrowsmith CH, Szyperski T, Montelione GT, Baker D, Bax A. Consistent blind protein structure generation from NMR chemical shift data. Proc Natl Acad Sci USA 2008;105:4685-4690.
18. Porto M, Bastolla U, Roman HE, Vendruscolo M. Reconstruction of protein structures from, a vectorial representation. Phys Rev Lett 2004;92:218101.
19. Bastolla U, Ortiz AR, Porto M, Teichert F. Effective connectivity profile: a structural representation that evidences the relationship between protein structures and sequences. Proteins 2008;73:872-888.
20. Teichert F, Bastolla U, Porto M. SABERTOOTH: protein structural alignment based on a vectorial structure representation. BMC Bioinformatics 2007:8:425.
21. Wolff K, Vendruscolo M, Porto M. Stochastic reconstruction of protein structures from effective connectivity profiles. PMC Biophys 2008; 1:5.
22. Jones D. Protein secondary structure prediction based on positionspecific scoring matrices. J Mol Biol 1999;292:195-202.
23. Vullo A, Walsh I, Pollastri G. A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics 2005; 7:180.
24. Zhang Y, Skolnick J. Scoring function for automated assessment of protein structure template quality. Proteins 2004;57:702-710.
25. CA.SP8 website. Available at: http://predictioncenter.org/download-area/ CASP8/se.rver-predictions (accessed on June 15, 2009).
26. Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W, Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-3402.
27. Wallin S, Farwer J, Bastolla U. Testing similarity measures with continuous and discrete protein models. Proteins 2002;50:144-157.
28. Rosetta forum. Available at: http://boinc.bakerlab.org/rosetta/forum- thread.php?i.d=1453#14335 (accessed on June 15, 2009).