References

• 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, 8, 477-496.

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:-

• Morris A L, MacArthur M W, Hutchinson E G & Thornton J M (1992). Stereochemical quality of protein structure coordinates. Proteins, 12, 345-364.

A statistical analysis of some protein NMR structures, and a description of the concepts of circular variance and notional resolution, are given in:-

• MacArthur M W & Thornton J M (1993). Conformational analysis of protein structures derived from NMR data. Proteins, 17, 232-251.

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 149-159.

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. In preparation.

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., 100, 1043-1047.