Acta Crystallographica Section D

Biological Crystallography

Volume 54, Part 6 Number 1 (November 1998)

Databases for macromolecular crystallography

Proceedings of the CCP4 study weekend, January 1998

A printed copy of this issue is available for purchase

Cover illustration: The balhimycin dimer, with citrate and acetate ions in the binding pockets, colour coded on a scale where the most mobile atoms are red and the least mobile are blue. The binding pockets are clearly the most mobile, consistent with the idea that they can open and close to complex with cell-wall binding peptides. Courtesy of George Sheldrick.

Acta Cryst. (1998). D54, 1065-1070    [DOI 10.1107/S0907444998009366]

The Globalization of Crystallographic Knowledge

P. Murray-Rust

Synopsis: The rapid growth of the World Wide Web provides major new opportunities for distributed databases, especially in macromolecular science. A new generation of technology, based on structured documents (SD) and XML, is being developed which will integrate documents and data in a seamless manner.

Online 1 November 1998

Acta Cryst. (1998). D54, 1071-1077    [DOI 10.1107/S0907444998007112]

Iditis: Protein Structure Database

S. Gardner and J. Thornton

Synopsis: The Iditis protein structure database provides the most comprehensive set of derived information about protein structure currently available and allows rapid searching for complex motifs.

Online 1 November 1998

Acta Cryst. (1998). D54, 1078-1084    [DOI 10.1107/S0907444998009378]

Protein Data Bank (PDB): Database of Three-Dimensional Structural Information of Biological Macromolecules

J. L. Sussman, D. Lin, J. Jiang, N. O. Manning, J. Prilusky, O. Ritter and E. E. Abola

Synopsis: The Protein Data Bank (PDB) at Brookhaven National Laboratory, a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries, is described.

Online 1 November 1998

Acta Cryst. (1998). D54, 1085-1094    [DOI 10.1107/S0907444998009846]

Macromolecular Structure Databases: Past Progress and Future Challenges

H. Weissig, I. N. Shindyalov and P. E. Bourne

Synopsis: A summary of macromlecular structure databases developed to date. The authors own work indicates that data are reported inconsistently and this should be addressed in the future.

Online 1 November 1998

Acta Cryst. (1998). D54, 1095-1104    [DOI 10.1107/S0907444998007926]

The Nucleic Acid Database: A Resource for Nucleic Acid Science

H. M. Berman, C. Zardecki and J. Westbrook

Synopsis: A description is given of how the Nucleic Acid Database (NDB) is used to study nucleic acids. In addition, the way in which the technology developed by the NDB project has been extended to macromolecules in general is summarized.

Online 1 November 1998

Acta Cryst. (1998). D54, 1105-1108    [DOI 10.1107/S0907444998008464]

Deposition of Macromolecular Structures

P. A. Keller, K. Henrick, P. McNeil, S. Moodie and G. J. Barton

Synopsis: A discussion is presented of some of the issues involved in depositing and releasing macromolecular structural information, and an outline of future directions.

Online 1 November 1998

The Role of Validation in Macromolecular Crystallography

E. Dodson

Synopsis: The importance of validation techniques in X-ray structure determination and their relation to refinement procedures are discussed, with particular reference to atomic resolution structures. The requirements of deposition and publication, and the role of validation tools in this are analysed. The need for a rigorously defined file format is emphasized.

Online 1 November 1998

Acta Cryst. (1998). D54, 1119-1131    [DOI 10.1107/S0907444998007100]

Databases in Protein Crystallography

G. J. Kleywegt and T. A. Jones

Synopsis: The use of databases for protein crystallographic model building, refinement, validation and analysis is reviewed, and some recent developments are discussed.

Online 1 November 1998

Acta Cryst. (1998). D54, 1132-1138    [DOI 10.1107/S0907444998007318]

New Tools and Resources for Analysing Protein Structures and Their Interactions

N. M. Luscombe, R. A. Laskowski, D. R. Westhead, D. Milburn, S. Jones, M. Karmirantzou and J. M. Thornton

Synopsis: A description of new analytical software tools and WWW servers for studying protein sequence, structure and function is presented.

Online 1 November 1998

Acta Cryst. (1998). D54, 1139-1146    [DOI 10.1107/S0907444998008324]

Protein Sequence Alignment Techniques

G. J. Barton

Synopsis: Algorithms for alignment of two or more protein sequences are described. Software for sequence analysis and database searching is summarized.

Online 1 November 1998

Acta Cryst. (1998). D54, 1147-1154    [DOI 10.1107/S0907444998009172]

SCOP, Structural Classification of Proteins Database: Applications to Evaluation of the Effectiveness of Sequence Alignment Methods and Statistics of Protein Structural Data

T. J. P. Hubbard, B. Ailey, S. E. Brenner, A. G. Murzin and C. Chothia

Synopsis: The Structural Classification of Proteins (SCOP) database is described. It provides a detailed and comprehensive description of the relationships of all known protein structures and can be used as a source of data to calibrate sequence search algorithms and for the generation of population statistics on protein structures.

Online 1 November 1998

Acta Cryst. (1998). D54, 1155-1167    [DOI 10.1107/S0907444998007501]

Classifying a Protein in the CATH Database of Domain Structures

C. A. Orengo, A. M. Martin, G. Hutchinson, S. Jones, D. J. Jones, A. D. Michie, M. B. Swindells and J. M. Thornton

Synopsis: The CATH database of protein domain structures classifies structures according to their (C)lass, (A)rchitecture, (T)opology or fold and (H)omologous family. Although the protocol used is mostly automatic, manual inspection is used to check assignments at some critical stages. Described in this article is a recently established facility to search the database with the coordinates of a newly determined structure.

Online 1 November 1998

Protein Three-Dimensional Structural Databases: Domains, Structurally Aligned Homologues and Superfamilies

R. Sowdhamini, D. F. Burke, C. Deane, J. - Huang, K. Mizuguchi, H. A. Nagarajaram, J. P. Overington, N. Srinivasan, R. E. Steward and T. L. Blundell

Synopsis: Databases of protein structural domains (DDBASE), aligned homologous protein structures (HOMSTRAD) and structurally aligned protein superfamilies (CAMPASS) are available on the WWW.

Online 1 November 1998

Acta Cryst. (1998). D54, 1178-1182    [DOI 10.1107/S0907444998007124]

Databases for Protein-Ligand Complexes

M. Hendlich

Synopsis: A survey of novel database tools for the analysis of protein-ligand interactions.

Online 1 November 1998

Acta Cryst. (1998). D54, 1183-1193    [DOI 10.1107/S0907444998008932]

Directional Preferences of Intermolecular Contacts to Hydrophobic Groups

J. C. Cole, R. Taylor and M. L. Verdonk

Synopsis: Analysis of data from the IsoStar library shows that many hydrophobic groups exhibit strikingly strong directional preferences in their intermolecular interactions. These directional preferences may need to be taken into account in parameterizing the next generation of protein-ligand docking programs.

Online 1 November 1998

Acta Cryst. (1998). D54, 1194-1198    [DOI 10.1107/S0907444998007744]

Metal Complex Geometries in Small-Molecule Crystals

A. G. Orpen

Synopsis: The reliability and transferability of M-L bond lengths and L-M-L bond angles from crystal structure is considered in the light of the utility of tables of `typical' bond lengths in transition-metal complexes.

Online 1 November 1998

Acta Cryst. (1998). D54, 1199-1206    [DOI 10.1107/S090744499800715X]

HAD, a Data Bank of Heavy-Atom Binding Sites in Protein Crystals: a Resource for Use in Multiple Isomorphous Replacement and Anomalous Scattering

S. A. Islam, D. Carvin, M. J. E. Sternberg and T. L. Blundell

Synopsis: The Heavy-Atom Data Bank (HAD) described contains coordinates of heavy-atom sites derived from multiple isomorphous derivatives used in protein crystallography. HAD contains information on crystallization conditions and protein binding sites that will be of value in the preparation of heavy-atom derivatives for use in preparation of isomorphous derivatives in the method of isomorphous replacement.

Online 1 November 1998