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

NMR-STAR

• NMR-STAR 3.2 Dictionary Documentation
• NMR-STAR 3.2 Dictionary Text (Git repository)
• NMR-STAR 3.1 PostgreSQL DDL script

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

Other data formats

• PDB file ATOM record example
• PDB format documentation
• mmCIF resources
• 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)