The reference for the AQUA and PROCHECK-NMR programs
- Laskowski R A, Rullmann J A C, MacArthur M W, Kaptein R, Thornton J M
(1996). AQUA and PROCHECK-NMR: Programs for checking the quality of
protein structures solved by NMR. Journal of Biomolecular NMR,
The reference for the original PROCHECK programs is:-
- Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993).
PROCHECK: a program to check the stereochemical quality of protein
structures. J. Appl. Cryst., 26, 283-291.
The statistical analyses that underlie the geometrical analyses performed
by PROCHECK are described in:-
A statistical analysis of some protein NMR structures, and a
description of the concepts of circular variance and notional
resolution, are given in:-
The G-factors calculated by PROCHECK-NMR are described in the
AQUA/PROCHECK-NMR paper cited above, but also in:
- Laskowski R A, MacArthur M W & Thornton J M (1994).
Evaluation of protein
coordinate data sets, in From First Map to Final Model, Proceedings
of the CCP4 study weekend, 6-7 January 1994, DL/SCI/R35, eds. Bailey S,
Hubbard R & Waller D, Daresbury Laboratory, Warrington, UK, pp
The reference for the Brookhaven Protein Data Bank (PDB) is:
- Bernstein F C, Koetzle T F, Williams G J B, Meyer E F Jr,
Brice M D, Rogers J R, Kennard O, Shimanouchi T & Tasumi M (1977). The
Protein Data Bank: a computer-based archival file for macromolecular
structures. J. Mol. Biol., 112, 535-542.
The IUPAC/IUBMB/IUPAB recommendations for the presentation of NMR
structures are given in:
- Arata Y, Bax A, Hilbers C W, Kaptein R, Markley J L, Sykes B D, Wright P
& Wüthrich K (1996).
Recommendations for presentation of NMR structures of proteins and nucleic
acids. IUPAC-IUBMB-IUPAB Interunion Task Group on the Standardisation
of Data Bases on Protein Structures by NMR in Solution.
The definitions of the Kabsch & Sander secondary structure
assignments are given in:-
Kabsch W & Sander C (1983).
Dictionary of protein secondary structure:
pattern recognition of hydrogen-bonded and geometrical features.
Biopolymers, 22, 2577-2637.
The reference for Ooi numbers is:-
Nishikawa K & Ooi T (1986).
Radial locations of amino-acid residues in a
globular protein - correlation with the sequence. J. Biochem.,