The Globalization of Crystallographic Knowledge

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.

Iditis: Protein Structure Database

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.

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

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.

Macromolecular Structure Databases: Past Progress and Future Challenges

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.

The Nucleic Acid Database: A Resource for Nucleic Acid Science

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.

Deposition of Macromolecular Structures

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

The Role of Validation in Macromolecular Crystallography

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.

Databases in Protein Crystallography

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

New Tools and Resources for Analysing Protein Structures and Their Interactions

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

Protein Sequence Alignment Techniques

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

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

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.

Classifying a Protein in the CATH Database of Domain Structures

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.

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

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

Databases for Protein–Ligand Complexes

A survey of novel database tools for the analysis of protein–ligand interactions.

Directional Preferences of Intermolecular Contacts to Hydrophobic Groups

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.

Metal Complex Geometries in Small-Molecule Crystals

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.

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

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.