Journal Article

FZJ-2014-04810

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Protein Structure Prediction: Assembly of Secondary Structure Elements by Basin-Hopping

Hoffmann, F.FZJ* ; Vancea, I.EMBL* ; Kamat, S. G. ; Strodel, B. (Corresponding Author)FZJ*

2014
Wiley-VCH Verl. Weinheim

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Please use a persistent id in citations: doi:10.1002/cphc.201402247

Abstract: The prediction of protein tertiary structure from primary structure remains a challenging task. One possible approach to this problem is the application of basin-hopping global optimization combined with an all-atom force field. In this work, the efficiency of basin-hopping is improved by introducing an approach that derives tertiary structures from the secondary structure assignments of individual residues. This approach is termed secondary-to-tertiary basin-hopping and benchmarked for three miniproteins: trpzip, trp-cage and ER-10. For each of the three miniproteins, the secondary-to-tertiary basin-hopping approach successfully and reliably predicts their three-dimensional structure. When it is applied to larger proteins, correctly folded structures are obtained. It can be concluded that the assembly of secondary structure elements using basin-hopping is a promising tool for de novo protein structure prediction.

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Contributing Institute(s):

1. Strukturbiochemie (ICS-6)

Research Program(s):

1. 452 - Structural Biology (POF2-452) (POF2-452)

Appears in the scientific report 2014

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Database coverage:
; Current Contents - Social and Behavioral Sciences ; JCR ; NCBI Molecular Biology Database ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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