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  • 1
    Electronic Resource
    Electronic Resource
    Rfree and the Rfree ratio. II. Calculation of the expected values and variances of cross-validation statistics in macromolecular least-squares refinement (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 442-450 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The free R factor is used routinely as a cross-validation tool in macromolecular crystallography. However, without any means of deriving quantitative estimates of its expected value and variance, its application has been rather subjective and its usefulness therefore somewhat limited. In the first part of this series, estimates of the expected value of the ratio of the free R factor to the standard R factor at the convergence of the structure refinement were given. Here, estimates of the variance of this ratio are given and are compared with the observed deviations from the expected values for a selection of refined structures. It is discussed how errors in the functional form of the structure-factor model as well as other types of errors might influence this ratio.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444999016868
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  • 2
    Electronic Resource
    Electronic Resource
    Error Estimates of Protein Structure Coordinates and Deviations from Standard Geometry by Full-Matrix Refinement of γB- and βB2-Crystallin (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 243-252 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Faster workstations with larger memories are making error estimation from full-matrix least-squares refinement a more practicable technique in protein crystallography. Using minimum variance weighting, estimated standard deviations of atomic positions have been calculated for two eye lens proteins from the inverse of a least-squares normal matrix which was full with respect to the coordinate parameters. γB-crystallin, refined at 1.49 Å yielded average errors in atomic positions which ranged from 0.05 Å for main-chain atoms to 0.27 Å for unrestrained water molecules. The second structure used in this work was that of βB2-crystallin refined at 2.1 Å resolution where the corresponding average errors were 0.08 and 0.35 Å, respectively. The relative errors in atomic positions are dependent on the number and kinds of restraints used in the refinements. It is also shown that minimum variance weighting leads to mean-square deviations from target geometry in the refined structures which are smaller than the variances used in the distance weighting.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499701041X
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  • 3
    Electronic Resource
    Electronic Resource
    Rfree and the Rfree Ratio. I. Derivation of Expected Values of Cross-Validation Residuals Used in Macromolecular Least-Squares Refinement (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 547-557 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The last five years have seen a large increase in the use of cross validation in the refinement of macromolecular structures using X-ray data. In this technique a test set of reflections is set aside from the working set and the progress of the refinement is monitored by the calculation of a free R factor which is based only on the excluded reflections. This paper gives estimates for the ratio of the free R factor to the R factor calculated from the working set for both unrestrained and restrained refinement. It is assumed that both the X-ray and restraint observations have been weighted correctly and that there is no correlation of errors between the test and working sets. It is also shown that the least-squares weights that minimize the variances of the refined parameters, also approximately minimize the free R factor. The estimated free R-factor ratios are compared with those reported for structures in the Protein Data Bank.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997013875
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  • 4
    Electronic Resource
    Electronic Resource
    New Tools and Resources for Analysing Protein Structures and Their Interactions (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 1132-1138 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The determination of protein structures has furthered our understanding of how various proteins perform their functions. With the large number of structures currently available in the PDB, it is necessary to be able to easily study these proteins in detail. Here new software tools are presented which aim to facilitate this analysis; these include the PDBsum WWW site which provides a summary description of all PDB entries, the programs TOPS and NUCPLOT to plot schematic diagrams representing protein topology and DNA-binding interactions, SAS a WWW-based sequence-analysis tool incorporating structural data, and WWW servers for the analysis of protein–protein interfaces and analyses of over 300 haem-binding proteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998007318
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  • 5
    Electronic Resource
    Electronic Resource
    AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR (1996)
    Springer
    Journal of biomolecular NMR 8 (1996), S. 477-486 
    Details
    ISSN: 1573-5001
    Keywords: Computer software ; Structure validation ; Restraint analysis ; Protein geometry
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Chemistry and Pharmacology
    Notes: Summary The 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 detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental data, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00228148
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  • 6
    Electronic Resource
    Electronic Resource
    Dihydrofolate reductase: A potential drug target in trypanosomes and leishmania (1998)
    Springer
    Journal of computer aided molecular design 12 (1998), S. 241-257 
    Details
    ISSN: 1573-4951
    Keywords: comparative molecular modelling ; dihydrofolate reductase ; drug design ; protein structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Dihydrofolate reductase has successfully been used as a drug target in the area of anti-cancer, anti-bacterial and anti-malarial chemotherapy. Little has been done to evaluate it as a drug target for treatment of the trypanosomiases and leishmaniasis. A crystal structure of Leishmania major dihydrofolate reductase has been published. In this paper, we describe the modelling of Trypanosoma cruzi and Trypanosoma brucei dihydrofolate reductases based on this crystal structure. These structures and models have been used in the comparison of protozoan, bacterial and human enzymes in order to highlight the different features that can be used in the design of selective anti-protozoan agents. Comparison has been made between residues present in the active site, the accessibility of these residues, charge distribution in the active site, and the shape and size of the active sites. Whilst there is a high degree of similarity between protozoan, human and bacterial dihydrofolate reductase active sites, there are differences that provide potential for selective drug design. In particular, we have identified a set of residues which may be important for selective drug design and identified a larger binding pocket in the protozoan than the human and bacterial enzymes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1016085005275
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  • 7
    Electronic Resource
    Electronic Resource
    Non-randomness in side-chain packing: the distribution of interplanar angles (1997)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 29 (1997), S. 370-380 
    Details
    ISSN: 0887-3585
    Keywords: protein interactions ; inter-residue ; side-chain packing ; protein folding ; hydrogen bonding ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: We analyze the distributions of interplanar angles between interacting side chains with well-defined planar regions, to see whether these distributions correspond to random packing or alternatively show orientational preferences. We use a non-homologous set of 79 high-resolution protein chain structures to show that the observed distributions are significantly different from the sinusoidal one expected for random packing. Overall, we see a relative excess of small angles and a paucity of large interplanar angles; the difference between the expected and observed distributions can be described as a shift of 5% of the interplanar angles from large (≥60°) to small (〈30°) values. By grouping the residue pairs into categories based on chemical similarity, we find that some categories have very non-sinusoidal interplanar angle distributions, whereas other categories have distributions that are close to sinusoidal. For a few categories, observed deviations from a sinusoidal distribution can be explained by the electrostatic anisotropy of the isolated pair potential energy. In other cases, the observed distributions reflect the longer range effects of different possible interaction geometries. In particular, geometries that disrupt external hydrogen bonding are disfavored. Proteins 29:370-380, 1997. © 1997 Wiley-Liss, Inc.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Use of parallel processing in the study of protein. Ligand binding (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 314-325 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have undertaken an energy minimization study of the binding of a small ligand, water, to amino acid side-chains. These calculations have been performed on a Meiko Computing surface containing a small number of transputers and on a larger transputer array installed at Edinburgh University. The aim of this study is twofold. First, we wished to compare these potential energy maps for a given side-chain as a function of the local secondary structure and also of the neighboring residue types. Secondly, the energy maps are found to be in good agreement with experimental distributions on the binding of water molecules to amino acid side-chains. The use of our in-house Meiko computing surface increases the speed of these calculations by a factor of about 25 over a VAX 11/750. With larger arrays of transputers, such as that at Edinburgh “concurrent” Supercomputer Project, we achieve increases in speed of over 200 such that these energy maps can be calculated at interactive speeds.
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110306
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