Improving a consensus approach for protein structure selection by removing redundancy

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 8, Issue 6, 2011, Pages 1708-1715

  Wang, Qingguo ^a   Shang, Yi ^a   Xu, Dong ^a  

^a University of Missouri   (United States)

Author keywords

consensus approach; Critical assessment of protein structure prediction; metapredictor; protein structure selection; Protein tertiary structure; quality assessment

Indexed keywords

CONSENSUS APPROACH; CRITICAL ASSESSMENT; METAPREDICTOR; PROTEIN STRUCTURE SELECTION; PROTEIN TERTIARY STRUCTURE; QUALITY ASSESSMENT;

MODEL STRUCTURES; RATING;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS;

EID: 80052907547     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.75     Document Type: Review

References (49)

1. J.G. Archie, M. Paluszewski, and K. Karplus, "Applying Undertaker to Quality Assessment," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 191-195, 2009.
2. D. Baker and A. Sali, "Protein Structure Prediction and Structural Genomics," Science, vol. 294, pp. 93-96, 2001. (Pubitemid 32952955)
3. M. Ben-David, O. Noivirt-Brik, A. Paz, J. Prilusky, J.L. Sussman, and Y. Levy, "Assessment of CASP8 Structure Predictions for Template Free Targets," Proteins: Structure, Function, and Bioinformatics, vol. 77, no. suppl 9, pp. 50-65, 2009.
4. P. Benkert, S.C.E. Tosatto, and D. Schomburg, "QMEAN: A Comprehensive Scoring Function for Model Quality Assessment," Proteins: Structure, Function, and Bioinformatics, vol. 71, pp. 261-277, 2008. (Pubitemid 351358609)
5. P. Benkert, S.C.E. Tosatto, and T. Schwede, "Global and Local Model Quality Estimation at CASP8 Using the Scoring Functions QMEAN and QMEANclust," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 173-180, 2009.
6. M.R. Betancourt and J. Skolnick, "Finding the Needle in a Haystack: Educing Protein Native Folds from Ambiguous ab initio Folding Predictions," J. Computational Chemistry, vol. 22, pp. 339-353, 2001. (Pubitemid 33645663)
7. R. Bondugula and D. Xu, "MUPRED: A Tool for Bridging the Gap between Template Based Methods and Sequence Profile Based Methods for Protein Secondary Structure Prediction," Proteins: Structure, Function, and Bioinfor-matics, vol. 66, pp. 664-670, 2007. (Pubitemid 46106770)
8. R. Bondugula, D. Xu, and Y. Shang, "A Fast Algorithm for Low-Resolution Protein Structure Prediction," Proc. Ann. Int'l Conf. IEEE Eng. in Medicine and Biology Soc., pp. 5826-5829, July 2006. (Pubitemid 46521243)
9. I. Borg and P. Groenen, Modern Multidimensional Scaling, Theory and Applications. Springer-Verlag, 1997.
10. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus, "CHARMM: A Program for Macromolecular Energy Minimization and Dynamic Calculations," J. Computational Chemistry, vol. 4, pp. 187-217, 1983.
11. J. Cheng, Z. Wang, A.N. Tegge, and J. Eickholt, "Prediction of Global and Local Quality of CASP8 Models by MULTICOM Series," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 181-184, 2009.
12. D. Cozzetto, A. Kryshtafovych, M. Ceriani, and A. Tramontano, "Assessment of Predictions in the Model Quality Assessment Category," Proteins: Structure, Function, and Bioinformatics, vol. 69, pp. 175-183, 2007. (Pubitemid 350210125)
13. D. Cozzetto, A. Kryshtafovych, and A. Tramontano, "Critical Assessment of Methods of Protein Structure Prediction-Round VIII," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 1-4, 2009.
14. D. Cozzetto, A. Kryshtafovych, and A. Tramontano, "Evaluation of CASP8 Model Quality Predictions," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 157-66, 2009.
15. K. Ginalski, A. Elofsson, D. Fischer, and L. Rychlewski, "3D-Jury: A Simple Approach to Improve Protein Structure Predictions," Bioinformatics, vol. 19, pp. 1015-1018, 2003. (Pubitemid 36675823)
16. C.H. Goulden, Methods of Statistical Analysis, second ed., pp. 50-55. Wiley, 1956.
17. D. Gront, U.H.E. Hansmann, and A. Kolinski, "Exploring Protein Energy Landscapes with Hierarchical Clustering," Int'l J. Quantum Chemistry, vol. 105, pp. 826-830, 2005. (Pubitemid 43082119)
18. M. Kalman and N. Ben-Tal, "Quality Assessment of Protein Model-Structures Using Evolutionary Conservation," Bioinformatics, vol. 26, no. 10, pp. 1299-1307, 2010.
19. D.E. Kim, D. Chivian, and D. Baker, "Protein Structure Prediction and Analysis Using the Robetta Server," Nucleic Acids Research, vol. 32, pp. 526-531, 2004.
20. D. Kozakov, K.H. Clodfelter, S. Vajda, and C.J. Camacho, "Optimal Clustering for Detecting near-Native Conformations in Protein Docking," Biophysical J., vol. 89, pp. 867-875, 2005. (Pubitemid 41098973)
21. T. Lazaridis and M. Karplus, "New View of Protein Folding Reconciled with the Old through Multiple Unfolding Simulations," Science, vol. 278, pp. 1928-1931, 1997. (Pubitemid 28013230)
22. P. Larsson, M.J. Skwark, B. Wallner, and A. Elofsson, "Assessment of Global and Local Model Quality in CASP8 Using Pcons and ProQ," Proteins: Structure, Function, and Bioinformatics, vol. 77, pp. 167-172, 2009.
23. M. Lu, A.D. Dousis, and J. Ma, "OPUS-PSP: An Orientation-Dependent Statistical All-Atom Potential Derived from Side-Chain Packing," J. Molecular Biology, vol. 376, pp. 288-301, 2008.
24. H. Lu and J. Skolnick, "A Distance-Dependent Atomic Knowledge-Based Potential for Improved Protein Structure Selection," Proteins: Structure, Function, and Genetics, vol. 44, pp. 223-232, 2001. (Pubitemid 32702231)
25. L.J. Mcguffin, "Prediction of Global and Local Model Quality in CASP8 Using the ModFOLD Server," Proteins: Structure, Function, and Bioinfor-matics, vol. 77, no. suppl 9, pp. 185-190, 2009.
26. L.J. McGuffin, "The ModFOLD Server for the Quality Assessment of Protein Structural Models," Bioinformatics, vol. 24, no. 4, pp. 586-587, 2008.
27. L.J. McGuffin and D.B. Roche, "Rapid Model Quality Assessment for Protein Structure Predictions Using the Comparison of Multiple Models without Structural Alignments," Bioinformatics, vol. 26, no. 2, pp. 182-188, 2010.
28. J. Moult, "Comparison of Database Potentials and Molecular Mechanics Force Fields," Current Opinion in Structural Biology, vol. 7, pp. 194-199, 1997. (Pubitemid 27156717)
29. I. Nobeli, J.B.O. Mitchell, A. Alex, and J. Thornton, "Evaluation of a Knowledge-Based Potential of Mean Force for Scoring Docked Protein-Ligand Complexes," J. Computational Chemistry, vol. 22, pp. 673-688, 2001. (Pubitemid 32442164)
30. J. Qui, W. Sheffler, D. Baker, and W.S. Noble, "Ranking Predicted Protein Structures with Support Vector Regression," Proteins: Structure, Function, and Bioinformatics, vol. 71, pp. 1175-1182, May 2008. (Pubitemid 351564044)
31. R. Samudrala and J. Moult, "An All-Atom Distance-Dependent Conditional Probability Discriminatory Function for Protein Structure Prediction," J. Molecular Biology, vol. 275, pp. 895-916, 1998. (Pubitemid 28077703)
32. M. Shen and A. Sali, "Statistical Potential for Assessment and Prediction of Protein Structures," Protein Science, vol. 15, pp. 2507-2524, 2006. (Pubitemid 44771688)
33. D. Shortle, K.T. Simons, and D. Baker, "Clustering of Low-Energy Conformations near the Native Structures of Small Proteins," Biophysics, vol. 95, pp. 11158-11162, 1998. (Pubitemid 28450098)
34. M. Sippl, "Knowledge-Based Potentials for Proteins," Current Opinion in Structural Biology, vol. 5, pp. 229-235, 1995.
35. K. Wang, B. Fain, M. Levitt, and R. Samudrala, "Improved Protein Structure Selection Using Decoy-Dependent Discriminatory Functions," BMC Structural Biology, vol. 4, p. 8, 2004.
36. Q. Wang, Y. Shang, and D. Xu, "A New Clustering-Based Method for Protein Structure Selection," Proc. Int'l Joint Conf. Neural Networks (IJCNN '08), pp. 2891-2898, 2008.
37. Z. Wang, A.N. Tegge, and J. Cheng, "Evaluating the Absolute Quality of a Single Protein Model Using Support Vector Machines and Structural Features," Proteins, vol. 75, no. 3, pp. 638-647, 2009.
38. B. Wallner and A. Elofsson, "Pcons5: Combining Consensus, Structural Evaluation and Fold Recognition Scores," Bioinformatics, vol. 21, pp. 4248-4254, 2005. (Pubitemid 41724304)
39. E.W. Weisstein, "Paired t-Test," From MathWorld-A Wolfram Web Resource, http://mathworld.wolfram.com/Pairedt-Test.html, 2011.
40. Y. Wu, M. Lu, M. Chen, J. Li, and J. Ma, "OPUS-Ca: A Knowledge-Based Potential Function Requiring Only Ca Positions," Protein Science, vol. 16, pp. 1449-1463, 2007. (Pubitemid 46984879)
41. C. Venclovas and M. Margelevicius, "Comparative Modeling in CASP6 Using Consensus Approach to Template Selection, Sequence-Structure Alignment, and Structure Assessment," Proteins: Structure, Function, and Bioinformatics, vol. 7, pp. 99-105, 2005. (Pubitemid 43069962)
42. Y. Zhang and J. Skolnick, "SPICKER: A Clustering Approach to Identify near-Native Protein Folds," J. Computational Chemistry, vol. 25, pp. 865-871, 2004.
43. Y. Zhang and J. Skolnick, "Scoring Function for Automated Assessment of Protein Structure Template Quality," Proteins, vol. 57, pp. 702-710, June 2004. (Pubitemid 39626992)
44. Y. Yang and Y. Zhou, "Ab initio Folding of Terminal Segments with Secondary Structures Reveals the Fine Difference between Two Closely Related All-Atom Statistical Energy Functions," Protein Science, vol. 17, pp. 1212-1219, 2008. (Pubitemid 351930918)
45. J. Zhang, Q. Wang, B. Barz, Z. He, I. Kosztin, Y. Shang, and D. Xu, "MUFOLD: A New Solution for Protein 3D Structure Prediction," Proteins: Structure, Function, and Bioinformatics, vol. 78, pp. 1137-1152, 2009.
46. A. Zemla, "LGA: A Method for Finding 3D Similarities in Protein Structures," Nucleic Acids Research, vol. 31, no. 13, pp. 3370-3374, 2003. (Pubitemid 37442162)
47. H. Zhou and Y. Zhou, "Distance-Scaled, Finite Ideal-Gas Reference State Improves Structure-Derived Potentials of Mean Force for Structure Selection and Stability Prediction," Protein Science, vol. 11, pp. 2714-2726, 2002. (Pubitemid 35191145)
48. http://prodata.swmed.edu/CASP8/evaluation/Categories.htm, 2011.
49. http://www.graphpad.com/quickcalcs/ttest1.cfm?Format=C, 2011.