NMRe : a web server for NMR protein structure refinement with high-quality structure validation scores

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Title
NMRe : a web server for NMR protein structure refinement with high-quality structure validation scores
Author(s)
Hyojung Ryu; GyuTae Lim; Bong Hyun SungJinhyuk Lee
Bibliographic Citation
Bioinformatics, vol. 32, no. 4, pp. 611-613
Publication Year
2016
Abstract
Summary: Protein structure refinement is a necessary step for the study of protein function. In particular, some nuclear magnetic resonance (NMR) structures are of lower quality than X-ray crystallographic structures. Here, we present NMRe, a web-based server for NMR structure refinement. The previously developed knowledge-based energy function STAP (Statistical Torsion Angle Potential) was used for NMRe refinement. With STAP, NMRe provides two refinement protocols using two types of distance restraints. If a user provides NOE (Nuclear Overhauser Effect) data, the refinement is performed with the NOE distance restraints as a conventional NMR structure refinement. Additionally, NMRe generates NOE-like distance restraints based on the inter-hydrogen distances derived from the input structure. The efficiency of NMRe refinement was validated on 20 NMR structures. Most of the quality assessment scores of the refined NMR structures were better than those of the original structures. The refinement results are provided as a three-dimensional structure view, a secondary structure scheme, and numerical and graphical structure validation scores. Availability and implementation: NMRe is available at http://psb.kobic.re.kr/nmre/ Contact: Supplementary information: Supplementary data are available at Bioinformatics online.
ISSN
1367-4803
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/bioinformatics/btv595
Type
Article
Appears in Collections:
Division of Biomaterials Research > Synthetic Biology and Bioengineering Research Center > 1. Journal Articles
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
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