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Proteins. 2014 Nov;82(11):3177-87. doi: 10.1002/prot.24685. Epub 2014 Sep 25.

Backbone dependency further improves side chain prediction efficiency in the Energy-based Conformer Library (bEBL).

Author information

1
Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706.

Abstract

Side chain optimization is an integral component of many protein modeling applications. In these applications, the conformational freedom of the side chains is often explored using libraries of discrete, frequently occurring conformations. Because side chain optimization can pose a computationally intensive combinatorial problem, the nature of these conformer libraries is important for ensuring efficiency and accuracy in side chain prediction. We have previously developed an innovative method to create a conformer library with enhanced performance. The Energy-based Library (EBL) was obtained by analyzing the energetic interactions between conformers and a large number of natural protein environments from crystal structures. This process guided the selection of conformers with the highest propensity to fit into spaces that should accommodate a side chain. Because the method requires a large crystallographic data-set, the EBL was created in a backbone-independent fashion. However, it is well established that side chain conformation is strongly dependent on the local backbone geometry, and that backbone-dependent libraries are more efficient in side chain optimization. Here we present the backbone-dependent EBL (bEBL), whose conformers are independently sorted for each populated region of Ramachandran space. The resulting library closely mirrors the local backbone-dependent distribution of side chain conformation. Compared to the EBL, we demonstrate that the bEBL uses fewer conformers to produce similar side chain prediction outcomes, thus further improving performance with respect to the already efficient backbone-independent version of the library.

KEYWORDS:

conformer; protein prediction; rotamer; side chain library; side chain optimization

PMID:
25212195
PMCID:
PMC4206580
DOI:
10.1002/prot.24685
[Indexed for MEDLINE]
Free PMC Article

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