TY - JOUR
T1 - STAP Refinement of the NMR database
T2 - A database of 2405 refined solution NMR structures
AU - Yang, Joshua Sung Woo
AU - Kim, Ji Han
AU - Oh, Sangho
AU - Han, Gukjeong
AU - Lee, Sanghyuk
AU - Lee, Jinhyuk
N1 - Funding Information:
Funding for open access charge: A grant from the ‘Korean Research Institute of Bioscience and Biotechnology Research Initiative Program’; and the Korean Ministry of Education, Science and Technology (MEST) under grant numbers 20110002321 and 20110019747, respectively.
PY - 2012/1
Y1 - 2012/1
N2 - 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, χ 1-χ 2 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.
AB - 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, χ 1-χ 2 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.
UR - http://www.scopus.com/inward/record.url?scp=84862188799&partnerID=8YFLogxK
U2 - 10.1093/nar/gkr1021
DO - 10.1093/nar/gkr1021
M3 - Article
C2 - 22102572
AN - SCOPUS:84862188799
SN - 0305-1048
VL - 40
SP - D525-D530
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -