LoopWeaver: Loop modeling by the weighted scaling of verified proteins

Journal of Computational Biology

Volumn 20, Issue 3, 2013, Pages 212-223

  Holtby, Daniel ^a   Li, Shuai Cheng ^b   Li, Ming ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b CITY UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

proteins

Indexed keywords

PROTEIN;

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

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS;

EID: 84874738439     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0078     Document Type: Article

References (26)

1. Basalaj, W. 2001. Proximity visualization of abstract data. Technical report, University of Cambridge Computer Laboratory Cambridge, United Kingdom.
2. Choi, Y., and Deane, C.M. 2010. Fread revisited: Accurate loop structure prediction using a database search algorithm. Proteins: Structure, Function, and Bioinformatics 78, 1431-1440.
3. Cohen, J.D. 1997. Drawing graphs to convey proximity: an incremental arrangement method. ACM Trans. Comput.-Hum. Interact. 4, 197-229.
4. Deane, C.M. and Blundell, T.L. 2001. Coda: A combined algorithm for predicting the structurally variable regions of protein models. Protein Science 10, 599-612.
5. de Bakker, P.I.W., DePristo, M.A., Burke, D.F., and Blundell, T.L. 2003. 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: Structure, Function, and Bioinformatics 51, 21-40.
6. de Leeuw, J. 1977. Applications of Convex Analysis to Multidimensional Scaling. In Barra J., Brodeau F., Romier G., and van Cutsem B., editors, Recent Developments in Statistics, 133-146. North Holland Publishing Company, Amsterdam.
7. Fiser, A., Do, R., and Sali, A. 2000. Modeling of loops in protein structures. Protein Science 9, 1753-1773.
8. Fiser, A., and Sali, A. 2003. Modeller: Generation and refinement of homology-based protein structure models. In Charles J., Carter W., and Sweet R.M., editors, Macromolecular Crystallography, Part D, Volume 374 of Methods in Enzymology, 461-491. Academic Press, Waltham, MA.
9. Hildebrand, P.W., Goede, A., Bauer, R.A. et al. 2009. SuperLoopera prediction server for the modeling of loops in globular and membrane proteins. Nucleic Acids Research 37, W571-W574.
10. Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
11. Kryshtafovych, A., Venclovas, C., Fidelis, K., and Moult, J. 2005. Progress over the first decade of casp experiments. Proteins 61, 225-236.
12. Lee, J., Lee, D., Park, H., et al. 2010. Protein loop modeling by using fragment assembly and analytical loop closure. Proteins: Structure, Function, and Bioinformatics 78, 3428-3436.
13. Mandell, D.J., Coutsias, E.A., and Kortemme, T. 2009. Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat. Methods 6, 551-552.
14. Mandell, D.J., and Pache, R.A. 2011. Rosetta projects: Documentation for kinematic loop modeling. Available online at http://rosettacommons.org/manuals/ archive/rosetta3.3y-usery-guide/appy-kinematicy-loopmodel.html Accessed Dec. 1, 2011.
15. Michalsky, E., Goede, A., and Preissner, R. 2003. Loops In Proteins (LIP) - a comprehensive loop database for homology modelling. Protein Engineering 16, 979-985.
16. Shenkin, P.S., Yarmush, D.L., Fine, R.M., et al. 1987. Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures. Biopolymers 26, 2053-2085.
17. Soto, C.S.S., Fasnacht, M., Zhu, J., et al. 2007. Loop modeling: sampling, filtering, and scoring. Proteins 70, 834-43.
18. Wang, C., Bradley, P., and Baker, D. 2007. Proteinprotein docking with backbone flexibility. Journal of Molecular Biology 373, 503-519.
19. Wang, G., and Dunbrack, R.L. 2003. PISCES: a protein sequence culling server. Bioinformatics 19, 1589-1591.
20. Xiang, Z., Soto, C.S., and Honig, B. 2002. Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. Proceedings of the National Academy of Sciences of the United States of America 99, 7432-7437.
21. Xu, J. 2005. Rapid protein side-chain packing via tree decomposition. In Miyano S., Mesirov J., Kasif S., et al. editors, Research in Computational Molecular Biology, Volume 3500 of Lecture Notes in Computer Science, 423-439. Springer Berlin / Heidelberg
22. Xu, J., and Berger, B. 2006. Fast and accurate algorithms for protein side-chain packing. J. ACM 53, 533-557.
23. Zhang, C., Liu, S., and Zhou, Y. 2004. Accurate and efficient loop selections by the dfire-based all-atom statistical potential. Protein Science 13, 391-399.
24. Zhang, J., Wang, Q., Barz, B., et al. 2010. Mufold: A new solution for protein 3d structure prediction. Proteins: Structure, Function, and Bioinformatics 78, 1137-1152.
25. Zhou, H., and Zhou, Y. 2002. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Science 11, 2714-2726.
26. Zhu, K., Pincus, D.L., Zhao, S., and Friesner, R.A. 2006. Long loop prediction using the protein local optimization program. Proteins: Structure, Function, and Bioinformatics 65, 438-452.