Fast algorithm for population-based protein structural model analysis

Proteomics

Volumn 13, Issue 2, 2013, Pages 221-229

  Zhang, Jingfen ^a   Xu, Dong ^a  

^a Department of Electrical Engineering and Computer Science   (United States)

Author keywords

Bioinformatics; Distance matrix; Dscore; Near native model selection; Protein model clustering; Visualization of distance distribution

Indexed keywords

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; MATHEMATICAL MODEL; POPULATION MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; QUALITATIVE ANALYSIS;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, CHEMICAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 84872683768     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201200334     Document Type: Article

References (29)

1. Baker, D., Sali, A., Protein structure prediction and structural genomics. Science 2001, 294, 93-96.
2. Floudas, C. A., Computational methods in protein structure prediction. Biotechnol. Bioeng. 2007, 97, 207-213.
3. Simons, K. T., 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.
4. Wu, S., Skolnick, J., Zhang, Y., Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 2007, 5, 17.
5. Hamelryck, T., Kent, J. T., Krogh, A., Sampling realistic protein conformations using local structural bias. PLoS Comput. Biol. 2006, 2, e131.
6. Bystroff, C., Shao, Y., Fully automated ab initio protein structure prediction using I-SITES, HMMSTR and ROSETTA. Bioinformatics 2002, 18(Suppl 1), S54-S61.
7. Go, N., Taketomi, H., Respective roles of short- and long-range interactions in protein folding. Proc. Natl. Acad. Sci. USA 1978, 75, 559-563.
8. Dobson, C. M., Šali, A., Karplus, M., Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. 1998, 37, 868-893.
9. Shortle, D., Simons, K. T., Baker, D., Clustering of low-energy conformations near the native structures of small proteins. Proc. Natl. Acad. Sci. USA 1998, 95, 11158-11162.
10. Roy, A., Kucukural, A., Zhang, Y., I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protocols 2010, 5, 725-738.
11. Betancourt, M. R., 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.
12. Zhang, Y., Skolnick, J., SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 2004, 25, 865-871.
13. Koehl, P., Protein structure similarities. Curr. Opin. Struct. Biol. 2001, 11, 348-353.
14. Kabsch, W., A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 1976, 32, 922-923.
15. Siew, N., Elofsson, A., Rychlewski, L., Fischer, D., MaxSub: an automated measure for the assessment of protein structure prediction quality. Bioinformatics 2000, 16, 776-785.
16. Zemla, A., LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res. 2003, 31, 3370-3374.
17. Zhang, Y., Skolnick, J., Scoring function for automated assessment of protein structure template quality. Proteins 2004, 57, 702-710.
18. Li, S. C., Ng, Y. K., Calibur: a tool for clustering large numbers of protein decoys. BMC Bioinformatics 2010, 11, 25.
19. Berenger, F., Zhou, Y., Shrestha, R., Zhang, K. Y., Entropy-accelerated exact clustering of protein decoys. Bioinformatics 2011, 27, 939-945.
20. Li, S. C., Bu, D., Li, M., Clustering 100, 000 protein structure decoys in minutes. IEEE/ACM Trans. Comput. Biol. Bioinform. 2012, 9, 765-773.
21. Li, H., Zhou, Y., SCUD: fast structure clustering of decoys using reference state to remove overall rotation. J. Comput. Chem. 2005, 26, 1189-1192.
22. Harder, T., Borg, M., Boomsma, W., Rogen, P., Hamelryck, T., Fast large-scale clustering of protein structures using Gauss integrals. Bioinformatics 2012, 28, 510-515.
23. Rogen, P., Bohr, H., A new family of global protein shape descriptors. Math. Biosci. 2003, 182, 167-181.
24. Holm, L., Sander, C., Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993, 233, 123-138.
25. Schwarz, G., Estimating the dimension of a model. Ann. Statist. 1978, 6, 461-464.
26. Zhang, J., Xu, D., Fast algorithm for clustering a large number of protein structural decoys. Bioinformatics and Biomedicine (BIBM), 2011 IEEE International Conference on 2011, pp. 30-36.
27. Clore, G. M., Robien, M. A., Gronenborn, A. M., Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 1993, 231, 82-102.
28. Doreleijers, J. F., Raves, M. L., Rullmann, T., Kaptein, R., Completeness of NOEs in protein structure: a statistical analysis of NMR. J. Biomol. NMR. 1999, 14, 123-132.
29. Gorgan, D., Bartha, A., Truta, A., Stefanut, T., Information Technology and Applications in Biomedicine, 2009. ITAB 2009. 9th International Conference on 2009, pp. 1-4.