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


METHODS
NMRe is available at http://psb.kobic.re.kr/nmre/.
Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, the Republic of Korea, Department of Nanobiotechnology and Bioinformatics, University of Science and Technology, Yuseong-Gu, Daejeon 305-350, the Republic of Korea and.
Hyojung
H
Ryu
Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, the Republic of Korea, Department of Nanobiotechnology and Bioinformatics, University of Science and Technology, Yuseong-Gu, Daejeon 305-350, the Republic of Korea and.
GyuTae
G
Lim
Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, the Republic of Korea.
Bong Hyun
BH
Sung
Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon 305-806, the Republic of Korea, Department of Nanobiotechnology and Bioinformatics, University of Science and Technology, Yuseong-Gu, Daejeon 305-350, the Republic of Korea and.
Jinhyuk
J
Lee
D020407:Internet; D051188:Knowledge Bases; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods*; D011487:Protein Conformation; D012984:Software