STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures

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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, 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.

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BioMagResBank

Eldon Ulrich, Hideo Akutsu, Jurgen F. Doreleijers … (2008)

The BioMagResBank (BMRB: www.bmrb.wisc.edu) is a repository for experimental and derived data gathered from nuclear magnetic resonance (NMR) spectroscopic studies of biological molecules. BMRB is a partner in the Worldwide Protein Data Bank (wwPDB). The BMRB archive consists of four main data depositories: (i) quantitative NMR spectral parameters for proteins, peptides, nucleic acids, carbohydrates and ligands or cofactors (assigned chemical shifts, coupling constants and peak lists) and derived data (relaxation parameters, residual dipolar couplings, hydrogen exchange rates, pKa values, etc.), (ii) databases for NMR restraints processed from original author depositions available from the Protein Data Bank, (iii) time-domain (raw) spectral data from NMR experiments used to assign spectral resonances and determine the structures of biological macromolecules and (iv) a database of one- and two-dimensional 1H and 13C one- and two-dimensional NMR spectra for over 250 metabolites. The BMRB website provides free access to all of these data. BMRB has tools for querying the archive and retrieving information and an ftp site (ftp.bmrb.wisc.edu) where data in the archive can be downloaded in bulk. Two BMRB mirror sites exist: one at the PDBj, Protein Research Institute, Osaka University, Osaka, Japan (bmrb.protein.osaka-u.ac.jp) and the other at CERM, University of Florence, Florence, Italy (bmrb.postgenomicnmr.net/). The site at Osaka also accepts and processes data depositions.

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Effective energy function for proteins in solution.

T Lazaridis, M Karplus (1999)

A Gaussian solvent-exclusion model for the solvation free energy is developed. It is based on theoretical considerations and parametrized with experimental data. When combined with the CHARMM 19 polar hydrogen energy function, it provides an effective energy function (EEF1) for proteins in solution. The solvation model assumes that the solvation free energy of a protein molecule is a sum of group contributions, which are determined from values for small model compounds. For charged groups, the self-energy contribution is accounted for primarily by the exclusion model. Ionic side-chains are neutralized, and a distance-dependent dielectric constant is used to approximate the charge-charge interactions in solution. The resulting EEF1 is subjected to a number of tests. Molecular dynamics simulations at room temperature of several proteins in their native conformation are performed, and stable trajectories are obtained. The deviations from the experimental structures are similar to those observed in explicit water simulations. The calculated enthalpy of unfolding of a polyalanine helix is found to be in good agreement with experimental data. Results reported elsewhere show that EEF1 clearly distinguishes correctly from incorrectly folded proteins, both in static energy evaluations and in molecular dynamics simulations and that unfolding pathways obtained by high-temperature molecular dynamics simulations agree with those obtained by explicit water simulations. Thus, this energy function appears to provide a realistic first approximation to the effective energy hypersurface of proteins.

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Biomolecules in the computer: Jmol to the rescue.

Ángel Herráez (2006)

Jmol is free, open source software for interactive molecular visualization. Since it is written in the Java™ programming language, it is compatible with all major operating systems and, in the applet form, with most modern web browsers. This article summarizes Jmol development and features that make it a valid and promising replacement for Rasmol and Chime in the development of educational materials, as well as in basic investigation of biomolecular structure. The description is set up by comparison with the well known abilities of Rasmol and Chime. Jmol is suitable for molecular model display and analysis in biochemistry, molecular biology, organic and inorganic chemistry, crystallography, and materials science. Copyright © 2006 International Union of Biochemistry and Molecular Biology, Inc.

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Journal

Journal ID (nlm-ta): Nucleic Acids Res

Journal ID (publisher-id): nar

Journal ID (hwp): nar

Title: Nucleic Acids Research

Publisher: Oxford University Press

ISSN (Print): 0305-1048

ISSN (Electronic): 1362-4962

Publication date Collection: January 2012

Publication date (Print): January 2012

Publication date (Electronic): 17 November 2011

Publication date PMC-release: 17 November 2011

Volume: 40

Issue: D1 , Database issue

Pages: D525-D530

Affiliations

¹Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro Yuseong-Gu, Daejeon 305-806, ²Department of Bioinformatics, University of Science and Technology, 217 Gajung-ro Yuseong-Gu, Daejeon 305-350 and ³Ewha Research Center for System Biology (ERCSB), Ewha Woman's University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, The Republic of Korea

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*To whom correspondence should be addressed. Tel: +82 42 879 8530; Fax: +82 42 879 8519; Email: jinhyuk@ 123456kribb.re.kr

Article

Publisher ID: gkr1021

DOI: 10.1093/nar/gkr1021

PMC ID: 3245188

PubMed ID: 22102572

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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

STAP Refinement of the NMR database: a database of 2405 refined solution NMR structures

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Genomic Prediction

Most cited references 22

BioMagResBank

Effective energy function for proteins in solution.

Biomolecules in the computer: Jmol to the rescue.

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