Loop modeling: Sampling, filtering, and scoring

Proteins: Structure, Function and Genetics

Volumn 70, Issue 3, 2008, Pages 834-843

  Soto, Cinque S ^a   Fasnacht, Marc ^a   Zhu, Jiang ^a   Forrest, Lucy ^a   Honig, Barry ^a  

^a Columbia University ^*  (United States)

Author keywords

DFIRE; Loop closure algorithm; Loop ensembles; Loop builder; LOOPY; OPLS force field

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; COMPUTER PROGRAM; ENERGY TRANSFER; FILTRATION; MOLECULAR MECHANICS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; SAMPLING; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

ALGORITHMS; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 38549154569     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21612     Document Type: Article

References (31)

1. Petrey D, Honig B. Protein structure prediction: inroads to biology. Mol Cell 2005;20:811-819.
2. Wang Z, Moult J. SNPs, protein structure, and disease. Hum Mutat 2001;17:263-270.
3. Fiser A. Protein structure modeling in the proteomics era. Expert Rev Proteomics 2004;1:97-110.
4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000;28:235-242.
5. Xiang BQ, Jia Z, Xiao FX, Zhou K, Liu P, Wei Q. The role of loop 7 in mediating calcineurin regulation. Protein Eng 2004;16:795-798.
6. Shi L, Javitch JA. The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice. Proc Natl Acad Sci USA 2004;101:440-445.
7. Nikiforovich GV, Marshall GR. Modeling flexible loops in the dark-adapted and activated states of rhodopsin, a prototypical G-protein-coupled receptor. Biophys J 2005;89:3780-3789.
8. Xiang Z, Soto CS, Honig B. Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction. Proc Natl Acad Sci USA 2002;99:7432-7437.
9. Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. A hierarchical approach to all-atom protein loop prediction. Proteins 2004;55:351-367.
10. Michalsky E, Goede A, Preissner R. Loops in proteins (LIP) - a comprehensive loop database for homology modelling. Protein Eng 2003;16:979-985.
11. Lessel U, Schomburg D. Importance of anchor group positioning in protein loop prediction. Proteins 1999;37:56-64.
12. Zhu K, Pincus DL, Zhao S, Friesner RA. Long loop prediction using the protein local optimization program. Proteins 2006;65:438-452.
13. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
14. Fiser A, Do RK, Sali A. Modeling of loops in protein structures. Protein Sci 2000;9:1753-1773.
15. de Bakker PI, DePristo MA, Burke DF, Blundell TL. Ab initio construction of polypeptide fragments: accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the generalized Born solvation model. Proteins 2003;51:21-40.
16. Shenkin PS, Yarmush DL, Fine RM, Wang HJ, Levinthal C. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers 1987;26:2053-2085.
17. DePristo MA, de Bakker PI, Lovell SC, Blundell TL. Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles. Proteins 2003;51:41-55.
18. Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916.
19. Smith KC, Honig B. Evaluation of the conformational free energies of loops in proteins. Proteins 1994;18:119-132.
20. Liu Z, Mao F, Li W, Han Y, Lai L. Calculation of protein surface loops using Monte-Carlo simulated annealing simulation. J Mol Modeling 2000;6:1-8.
21. Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004;383:66-93.
22. Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
23. Zhang C, Liu S, Zhou Y. Accurate and efficient loop selections by the DFIRE-based all-atom statistical potential. Protein Sci 2004;13:391-399.
24. Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
25. Cahill S, Cahill M, Cahill K. On the kinematics of protein folding. J Comput Chem 2003;24:1364-1370.
26. Xiang Z. Advances in Homology Modeling. PhD thesis, Columbia University; 2000.
27. Xiang Z, Honig B. Extending the accuracy limits of prediction for side-chain conformations. J Mol Biol 2001;311:421-430.
28. Engh RA, Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Cryst 1991;47:392-400.
29. Schweiters CD, Kuszewski JJ, Tjandra N, Clore GM. The Xplor-NIH NMR molecular structure determination package. J Magn Reson 2003;160:66-74.
30. Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: local sampling, knowledge-based potentials, and clustering. Proteins 2006;65:463-479.
31. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1983;4:187-217.