|
Biological Magnetic Resonance Data BankA Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules |
Member of
|
Standards and Data Formats
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 standardsIndirect 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
- summary figure
- chemical shift data - downloaded Excel file
- pH titration data - downloaded Excel file
- supplemental material
Sequential and medium-range proton distances in polypeptide secondary structures
NMR-STARNMR-STAR 3.2 Dictionary Documentation
NMR-STAR 3.2 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)
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)
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