A simple probabilistic model of multibody interactions in proteins
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A simple probabilistic model of multibody interactions in proteins. / Johansson, Kristoffer Enøe; Hamelryck, Thomas.
In: Proteins: Structure, Function, and Bioinformatics, Vol. 81, No. 8, 2013, p. 1340-1350.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - A simple probabilistic model of multibody interactions in proteins
AU - Johansson, Kristoffer Enøe
AU - Hamelryck, Thomas
N1 - Copyright © 2013 Wiley Periodicals, Inc., a Wiley company.
PY - 2013
Y1 - 2013
N2 - Protein structure prediction methods typically use statistical potentials, which rely on statistics derived from a database of know protein structures. In the vast majority of cases, these potentials involve pairwise distances or contacts between amino acids or atoms. Although some potentials beyond pairwise interactions have been described, the formulation of a general multibody potential is seen as intractable due to the perceived limited amount of data. In this article, we show that it is possible to formulate a probabilistic model of higher order interactions in proteins, without arbitrarily limiting the number of contacts. The success of this approach is based on replacing a naive table-based approach with a simple hierarchical model involving suitable probability distributions and conditional independence assumptions. The model captures the joint probability distribution of an amino acid and its neighbors, local structure and solvent exposure. We show that this model can be used to approximate the conditional probability distribution of an amino acid sequence given a structure using a pseudo-likelihood approach. We verify the model by decoy recognition and site-specific amino acid predictions. Our coarse-grained model is compared to state-of-art methods that use full atomic detail. This article illustrates how the use of simple probabilistic models can lead to new opportunities in the treatment of nonlocal interactions in knowledge-based protein structure prediction and design.
AB - Protein structure prediction methods typically use statistical potentials, which rely on statistics derived from a database of know protein structures. In the vast majority of cases, these potentials involve pairwise distances or contacts between amino acids or atoms. Although some potentials beyond pairwise interactions have been described, the formulation of a general multibody potential is seen as intractable due to the perceived limited amount of data. In this article, we show that it is possible to formulate a probabilistic model of higher order interactions in proteins, without arbitrarily limiting the number of contacts. The success of this approach is based on replacing a naive table-based approach with a simple hierarchical model involving suitable probability distributions and conditional independence assumptions. The model captures the joint probability distribution of an amino acid and its neighbors, local structure and solvent exposure. We show that this model can be used to approximate the conditional probability distribution of an amino acid sequence given a structure using a pseudo-likelihood approach. We verify the model by decoy recognition and site-specific amino acid predictions. Our coarse-grained model is compared to state-of-art methods that use full atomic detail. This article illustrates how the use of simple probabilistic models can lead to new opportunities in the treatment of nonlocal interactions in knowledge-based protein structure prediction and design.
U2 - 10.1002/prot.24277
DO - 10.1002/prot.24277
M3 - Journal article
C2 - 23468247
VL - 81
SP - 1340
EP - 1350
JO - Proteins: Structure, Function, and Bioinformatics
JF - Proteins: Structure, Function, and Bioinformatics
SN - 0887-3585
IS - 8
ER -
ID: 46019085