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PROCHECK: a program to check the stereochemical quality of protein structures
The PROCHECK suite of programs provides a detailed check on the stereochemistry of a protein structure. Its outputs comprise a number of plots in PostScript format and a comprehensive… Expand
The rapid generation of mutation data matrices from protein sequences
An efficient means for generating mutation data matrices from large numbers of protein sequences is presented, by means of an approximate peptide-based sequence comparison algorithm, which is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fastenough to generate a matrix from a specific family or class of proteins in minutes. Expand
AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
- R. Laskowski, J. Rullmann, M. W. Macarthur, R. Kaptein, J. Thornton
- Chemistry, Medicine
- Journal of biomolecular NMR
- 1 December 1996
SummaryThe AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a… Expand
LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions.
- A. C. Wallace, R. Laskowski, J. Thornton
- Computer Science, Medicine
- Protein engineering
- 1 February 1995
The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. Expand
CATH--a hierarchic classification of protein domain structures.
- C. Orengo, A. Michie, S. Jones, D. T. Jones, M. Swindells, J. Thornton
- Biology, Medicine
- 15 August 1997
Analysis of the structural families generated by CATH reveals the prominent features of protein structure space and a database of well-characterised protein structure families will facilitate the assignment of structure-function/evolution relationships to both known and newly determined protein structures. Expand
Satisfying hydrogen bonding potential in proteins.
The frequency with which potential hydrogen bond donors and acceptors are satisfied in protein molecules is analysed and it is found that as the resolution of the data improves, the percentages fall. Expand
Main-chain bond lengths and bond angles in protein structures.
The main-chain bond lengths and bond angles of protein structures are analysed as a function of resolution and differences in means are found to be highly statistically significant, suggesting that the different target values used by the different methods leave their imprint on the structures they refine. Expand
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
The Catalytic Site Atlas (CSA) provides catalytic residue annotation for enzymes in the Protein Data Bank with an original hand-annotated set containing information extracted from the primary literature, using defined criteria to assign catalytic residues. Expand
Stereochemical quality of protein structure coordinates
The parameters used in this evaluation are not novel, and are easily calculated from structure coordinates, which provide a simple guide as to the reliability of a structure, in addition to the most important measures, resolution and R‐factor. Expand
Principles of protein-protein interactions.
- S. Jones, J. Thornton
- Medicine, Chemistry
- Proceedings of the National Academy of Sciences…
- 9 January 1996
This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The… Expand