BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

Standards and Data Formats

Nomenclature and macromolecular residue references

Amino acid atom nomenclature conversion table

Amino acid pseudoatom nomenclature conversion table

Nucleic acid pseudoatom nomenclature conversion table

Atom nomenclature - proton nomenclature for amino acids and nucleic acids

Amino acid browser - atom nomenclature, structure, properties, abbreviations, and for the 20 common L- amino acids

Amino acid table references - helix/sheet propensities, pKa values, codons, abbreviations, hydrophobicity, and molecular weights in table formats

Protein calculator - estimates pI, charge, UV absorbance, etc. From the Scripps Research Institute

Experimentally defined standards

Indirect chemical shift referencing ratios

Standard amino acid 1H, 13C, and 15N chemical shifts - Dyson, Wright, and coworkers

Standard amino acid 1H and 13C chemical shifts - Wüthrich and coworkers

Chemical shift index parameters for amino acids (tar file) - Dyson, Wright, and coworkers (brief documentation)

Chemical shift index parameters for amino acids - Wishart and coworkers

pH dependent amino acid chemical shifts - Platzer, Okon, and McIntosh

Sequential and medium-range proton distances in polypeptide secondary structures

Secondary structure backbone proton-proton NOE intensities and secondary structure H-alpha to NH coupling constants

NMR-STAR

NMR-STAR 3.1 Dictionary Documentation

NMR-STAR 3.1 Dictionary Text (subversion repository)

NMR-STAR 3.1 PostgreSQL DDL script

NMR-STAR 2.1 (legacy format) simple schema

NMR-STAR 2.1 (legacy format) complete annotated schema

NMR-STAR 2.1 (legacy format) database schema and layout of the files
and ASCII database table dumps (obsolete and unmaintained)

Other data formats

PDB file ATOM record example

PDB format documentation

mmCIF resources

PDB eXchange mmCIF dictionary

CCPN Data Model

X-PLOR Manual

IUPAC recommendations

IUPAC Recommendations 1997
R. K. Harris, J. Kowalewski, and S. C. De Menezes;
"Parameters and Symbols for use in Nuclear Magnetic Resonance", Pure & Appl. Chem. 69, 2489-2495 (1997).
DOI: 10.1351/pac199769122489

IUPAC Recommendations 1998
J. L. Markley, A. Bax, Y. Arata, C. W. Hilbers, R. Daptein, B. D. Sykes, P. E Wright, and K. Wüthrich;
"Recommendations for the Presentation of NMR Structures of Proteins and Nucleic Acids", Pure & Appl. Chem. 70, 117-142 (1998).
DOI: 10.1351/pac199870010117 (PDF)

IUPAC Recommendations 2001
R. K. Harris, E. D. Becker, S. M. Cabral de Menezes, R. Goodfellow, and P. Granger;
"NMR nomenclature. Nuclear spin properties and conventions for chemical shifts", Pure & Appl. Chem. 73, 1795-1818 (2001).
DOI: 10.1351/pac200173111795

IUPAC Recommendations 2008
R. K. Harris, E. D. Becker, S. M. Cabral de Menezes, P. Granger, R. E. Hoffman, and K. W. Zilm;
"Further Conventions for NMR Shielding and Chemical Shifts", Pure & Appl. Chem. 80, No. 1, 59-84 (2008).
DOI: 10.1351/pac200880010059 (PDF)

Publications describing the STAR format

Hall, S. R.,
"The STAR File: A New Format for Electronic Data Transfer and Archiving",
J. Chem. Inf. Comput. Sci. 31, 326-333 (1991).
DOI: 10.1021/ci00002a020

Hall, S. R. and Spadaccini, N.,
"The STAR File: Detailed Specifications",
J. Chem. Inf. Comput. Sci. 34, 505-508 (1994).
DOI: 10.1021/ci00019a005

Hall, S. R. and Cook, A. P. F.,
"STAR Dictionary Definition Language: Initial Specification",
J. Chem. Inf. Comput. Sci. 35, 819-825 (1995).
DOI: 10.1021/ci00027a005

Allen, F. H., Barnard, J. M., Cook, A. P. F., and Hall, S. R.,
"The Molecular Information File (MIF): Core Specifications of a New Standard Format for Chemical Data",
J. Chem. Inf. Comput. Sci. 35, 412-427 (1995).
DOI: 10.1021/ci00025a009

Spadaccini, N. and Hall, S. R.,
"Extensions to the STAR File Syntax"
J. Chem. Inf. Model., 52 (8), 1901-1906 (2012)
DOI: 10.1021/ci300074v

Spadaccini, N., Castleden, I. R., du Boulayand, D. and Hall, S. R.,
"dREL: A Relational Expression Language for Dictionary Methods"
J. Chem. Inf. Model., 52 (8), 1917-1925 (2012)
DOI: 10.1021/ci300076w