Journal Article

FZJ-2015-07317

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Protein structure refinement with adaptively restrained homologous replicas

Della Corte, D.FZJ* ; Wildberg, A. ; Schröder, G. (Corresponding author)FZJ*

2016
Wiley-Liss New York, NY

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Please use a persistent id in citations: doi:10.1002/prot.24939

Abstract: A novel protein refinement protocol is presented which utilizes molecular dynamics (MD) simulations of an ensemble of adaptively restrained homologous replicas. This approach adds evolutionary information to the force field and reduces random conformational fluctuations by coupling of several replicas. It is shown that this protocol refines the majority of models from the CASP11 refinement category and that larger conformational changes of the starting structure are possible than with current state of the art methods. The performance of this protocol in the CASP11 experiment is discussed. We found that the quality of the refined model is correlated with the structural variance of the coupled replicas, which therefore provides a good estimator of model quality. Furthermore, some remarkable refinement results are discussed in detail.

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Contributing Institute(s):

1. Strukturbiochemie (ICS-6)
2. JARA - HPC (JARA-HPC)

Research Program(s):

1. 551 - Functional Macromolecules and Complexes (POF3-551) (POF3-551)
2. Critical Assessment of Protein Structure Prediction 11 (jics66_20140501) (jics66_20140501)

Appears in the scientific report 2016

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Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; No Authors Fulltext ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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