Discriminative learning for protein conformation sampling.

Proteins
Feng ZhaoJinbo Xu

Abstract

Protein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Conditional Random Fields (CRFs). Using a discriminative learning method, CRFSampler can automatically learn more than ten thousand parameters quantifying the relationship among primary sequence, secondary structure, and (pseudo) backbone angles. Using only compactness and self-avoiding constraints, CRFSampler can efficiently generate protein-like conformations from primary sequence and predicted secondary structure. CRFSampler is also very flexible in that a variety of model topologies and feature sets can be defined to model the sequence-structure relationship without worrying about parameter estimation. Our experimental results demonstrate that using a simple set of features, CRFSampler can generate decoys with much higher quality than the most recent HMM model.

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Citations

Jun 30, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Feng ZhaoJinbo Xu
Aug 29, 2012·Briefings in Bioinformatics·Mehdi MaadooliatJianhua Z Huang
Mar 17, 2010·BMC Bioinformatics·Martin Paluszewski, Thomas Hamelryck
Jul 26, 2012·PloS One·David SimonciniKam Y J Zhang
Mar 23, 2011·Theoretical Chemistry Accounts·Yaoqi ZhouHongxing Lei
Dec 24, 2015·Journal of Computational Chemistry·Yuedong Yang, Yaoqi Zhou
Aug 30, 2008·Protein Science : a Publication of the Protein Society·Shuai Cheng LiMing Li
Sep 2, 2009·Proteins·Jinbo XuFeng Zhao
Jun 4, 2013·Journal of Computational Chemistry·Priyanka Dhingra, Bhyravabhotla Jayaram
Mar 8, 2013·Proteins·Kristoffer Enøe Johansson, Thomas Hamelryck
Jun 6, 2015·Biochimie·Guillaume PosticJean-Christophe Gelly
Nov 7, 2015·Scientific Reports·Debswapna Bhattacharya, Jianlin Cheng
Jan 13, 2010·Protein Science : a Publication of the Protein Society·Joe DeBartoloTobin R Sosnick
Dec 4, 2020·PloS One·Andrew J McGeheeDebswapna Bhattacharya
Aug 25, 2020·Computational and Structural Biotechnology Journal·Guillaume PosticGautier Moroy

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