NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments

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Abstract

The growth of the biological nuclear magnetic resonance (NMR) field and the development of new experimental technology have mandated the revision and enlargement of the NMR-STAR ontology used to represent experiments, spectral and derived data, and supporting metadata. We present here a brief description of the NMR-STAR ontology and software tools for manipulating NMR-STAR data files, editing the files, extracting selected data, and creating data visualizations. Detailed information on these is accessible from the links provided.

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NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

Woonghee Lee, Marco Tonelli, John Markley (2014)

Summary: SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. Availability and implementation: The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

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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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Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

G Cornilescu, F Delaglio, A. Bax (1999)

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C alpha, 13C beta, 13C', 1H alpha and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar phi and psi backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 degrees. Approximately 3% of the predictions made by TALOS are found to be in error.

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Author and article information

Journal

Journal ID (nlm-journal-id): 9110829

Journal ID (pubmed-jr-id): 2209

Journal ID (nlm-ta): J Biomol NMR

Journal ID (iso-abbrev): J. Biomol. NMR

Title: Journal of biomolecular NMR

ISSN (Print): 0925-2738

ISSN (Electronic): 1573-5001

Publication date Nihms-submitted: 12 February 2019

Publication date (Electronic): 22 December 2018

Publication date (Print): February 2019

Publication date PMC-release: 31 March 2019

Volume: 73

Issue: 1-2

Pages: 5-9

Affiliations

[1 ]Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA

[2 ]Department of Computer Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA

[3 ]ATHENA Research and Innovation Center, Athens, Greece

[4 ]Department of Molecular Biology and Biophysics, UConn Health, 263 Farmington Avenue, Farmington, CT 06030, USA

Author notes

Author contributions ELU developed the NMR-STAR ontology, KB developed RBMRB and other software tools for creating and working with NMR-STAR, YEI, assisted with the relational schema, ML, advised on software development, PRP lead the BMRB project, DM developed validation tools, JRW, developed PyNMRSTAR and other software tools, HY evaluated tools for deposition annotation, HRE directed software development, JLM, heads BMRB; JCH heads NMR-box. All authors assisted in the preparation of the manuscript.

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John L. Markley http://orcid.org/0000-0003-1799-6134

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Manuscript ID: NIHMS1007768

DOI: 10.1007/s10858-018-0220-3

PMC ID: 6441402

PubMed ID: 30580387

SO-VID: 9e464a38-b34d-4395-818e-9a8079f82f59

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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments

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Most cited references 22

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

BioMagResBank

Protein backbone angle restraints from searching a database for chemical shift and sequence homology.

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