TY - JOUR

T1 - Formulation of probabilistic models of protein structure in atomic detail using the reference ratio method

AU - Valentin, Jan

AU - Andreetta, Christian

AU - Boomsma, Wouter Krogh

AU - Bottaro, Sandro

AU - Ferkinghoff-Borg, Jesper

AU - Frellsen, Jes

AU - Mardia, Kanti V.

AU - Tian, Pengfei

AU - Hamelryck, Thomas Wim

N1 - Copyright © 2013 Wiley Periodicals, Inc., a Wiley company.

PY - 2014

Y1 - 2014

N2 - We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.

AB - We propose a method to formulate probabilistic models of protein structure in atomic detail, for a given amino acid sequence, based on Bayesian principles, while retaining a close link to physics. We start from two previously developed probabilistic models of protein structure on a local length scale, which concern the dihedral angles in main chain and side chains, respectively. Conceptually, this constitutes a probabilistic and continuous alternative to the use of discrete fragment and rotamer libraries. The local model is combined with a nonlocal model that involves a small number of energy terms according to a physical force field, and some information on the overall secondary structure content. In this initial study we focus on the formulation of the joint model and the evaluation of the use of an energy vector as a descriptor of a protein's nonlocal structure; hence, we derive the parameters of the nonlocal model from the native structure without loss of generality. The local and nonlocal models are combined using the reference ratio method, which is a well-justified probabilistic construction. For evaluation, we use the resulting joint models to predict the structure of four proteins. The results indicate that the proposed method and the probabilistic models show considerable promise for probabilistic protein structure prediction and related applications. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.

U2 - 10.1002/prot.24386

DO - 10.1002/prot.24386

M3 - Journal article

C2 - 23934827

VL - 82

SP - 288

EP - 299

JO - Proteins: Structure, Function, and Bioinformatics

JF - Proteins: Structure, Function, and Bioinformatics

SN - 0887-3585

IS - 2

ER -