Improving predicted protein loop structure ranking using a Pareto-optimality consensus method.

BMC Structural Biology
Yaohang LiEric Jakobsson

Abstract

Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. We have developed a Pareto Optimal Consensus (POC) method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1) identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2) ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of approximately 20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring f...Continue Reading

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Citations

Jun 28, 2011·Journal of Chemical Information and Modeling·Yaohang LiEric Jakobsson
Jul 24, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Rudy Clausen, Amarda Shehu
Mar 15, 2015·Journal of Molecular Graphics & Modelling·Michael FeigYuji Sugita
Jan 1, 2013·Computational and Structural Biotechnology Journal·Yaohang Li
Jan 1, 2011·Journal of Mathematical Chemistry·Dorota Bielińska-Wąż
Aug 10, 2019·Journal of Theoretical Biology·Gaoshi LiJianxin Wang

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Methods Mentioned

BETA
NMR
protein folding

Software Mentioned

Parento
SGB
AA Rosetta
Rosetta
CHARMM
OPLS
POC
DDFIRE
DFIRE
DOPE

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