STAP refinement of the NMR database: a database of 2405 refined solution NMR structures = STAP NMR 구조개선 데이타베이스

Cited 19 time in scopus
Metadata Downloads
Title
STAP refinement of the NMR database: a database of 2405 refined solution NMR structures = STAP NMR 구조개선 데이타베이스
Author(s)
Joshua Yang; Jihan Kim; Sang Ho Oh; Gukjeong Han; Sanghyuk Lee; Jinhyuk Lee
Bibliographic Citation
Nucleic Acids Research, vol. 40, no. D, pp. D525-D530
Publication Year
2012
Abstract
According to several studies, some nuclear magnetic resonance (NMR) structures are of lower quality, less reliable and less suitable for structural analysis than high-resolution X-ray crystallographic structures. We present a public database of 2405 refined NMR solution structures [statistical torsion angle potentials (STAP) refinement of the NMR database, http://psb.kobic.re.kr/STAP/refinement] from the Protein Data Bank (PDB). A simulated annealing protocol was employed to obtain refined structures with target potentials, including the newly developed STAP. The refined database was extensively analysed using various quality indicators from several assessment programs to determine the nuclear Overhauser effect (NOE) completeness, Ramachandran appearance, χ1-χ2 rotamer normality, various parameters for protein stability and other indicators. Most quality indicators are improved in our protocol mainly due to the inclusion of the newly developed knowledge-based potentials. This database can be used by the NMR structure community for further development of research and validation tools, structure-related studies and modelling in many fields of research.
ISSN
0305-1048
Publisher
Oxford Univ Press
DOI
http://dx.doi.org/10.1093/nar/gkr1021
Type
Article
Appears in Collections:
Division of Biomedical Research > Genome Editing Research Center > 1. Journal Articles
Files in This Item:
  • There are no files associated with this item.


Items in OpenAccess@KRIBB are protected by copyright, with all rights reserved, unless otherwise indicated.