Minimizing and learning energy functions for side-chain prediction

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Chen YanoverYair Weiss

Abstract

Side-chain prediction is an important subproblem of the general protein folding problem. Despite much progress in side-chain prediction, performance is far from satisfactory. As an example, the ROSETTA program that uses simulated annealing to select the minimum energy conformations, correctly predicts the first two side-chain angles for approximately 72% of the buried residues in a standard data set. Is further improvement more likely to come from better search methods, or from better energy functions? Given that exact minimization of the energy is NP hard, it is difficult to get a systematic answer to this question. In this paper, we present a novel search method and a novel method for learning energy functions from training data that are both based on Tree Reweighted Belief Propagation (TRBP). We find that TRBP can obtain the global optimum of the ROSETTA energy function in a few minutes of computation for approximately 85% of the proteins in a standard benchmark set. TRBP can also effectively bound the partition function which enables using the Conditional Random Fields (CRF) framework for learning. Interestingly, finding the global minimum does not significantly improve side-chain prediction for an energy function based on ...Continue Reading

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Citations

May 29, 2010·Molecular & Cellular Proteomics : MCP·Keren LaskerAndrej Sali
Jul 17, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Marcos R Betancourt
Jan 20, 2011·Bioinformatics·Anna Katharina DehofAndreas Hildebrandt
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Jun 8, 2010·BMC Bioinformatics·Tim HarderThomas Hamelryck
Feb 26, 2014·BMC Structural Biology·Yajia Zhang, Kris Hauser
Jan 5, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Yao-Ming Huang, Christopher Bystroff
Apr 27, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Shuai Cheng LiMing Li
Mar 8, 2016·Proteins·Thomas GaillardThomas Simonson
Oct 16, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Paul SwobodaBogdan Savchynskyy
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Jul 14, 2010·Journal of Computational Chemistry·Oz SharabiJulia M Shifman
Jan 26, 2011·Journal of Computational Chemistry·Albert H Ng, Christopher D Snow
Dec 4, 2012·Journal of Chemical Information and Modeling·Woong-Hee Shin, Chaok Seok

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