(1) Unite de Conformation de Macromolecules Biologiques, Universite
Libre de Bruxelles, CP160-16, Ave. F. Roosevelt, 1050 Bruxelles;
(2) EMBL-EBI, Welcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
Managing the information on bio-macromolecules sequences and structures has become one of the major challenges of modern molecular biology. In the case of protein 3D structure the problem is difficult, because it involves handling a wealth of complex information, some of which must be computed from the atomic coordinates, by applying specialized programs. More specifically, the data needs to be validated, i.e. the quality and consistency of the data must be assessed. To promote scientific progress, structural information must be integrated with data obtained from different sources, for instance, data on sequence, function, gene structure, and phylogeny, and of course, the data must be readily and widely accessible. Here, we review the relational database (SESAM), implemented under SYBASE (Huysmans et al., 1991), designed to cater to some of the above needs. In addition we describe tools for analyzing and validating the atomic coordinates of protein crystal structures. One is the program PROVE, which evaluates the quality of a protein crystal structure by analyzing atomic volumes (Pontius et al., 1996). The other is SF_CHECK, a program that analyzes experimental structure factor data and evaluates the agreement of the model with these data using a set of objective criteria (Wodak et al. 1997).
References
Huysmans M., Richelle J. and Wodak S.J. (1991), SESAM: a relational
database for structures of macromolecules Proteins: Struct., Funct.,
Genet. 11 (1), 59-76
Pontius J., Richelle J. and Wodak S.J. (1996), Deviations from
standard atomic volumes as a quality measure for protein crystal
structures, J. Mol. Biol. in press
Wodak S.J., Pontius J., Vaguine A. and Richelle J. (1997), in the
Proceedings of the macro molecular crystallography computing school,
Seattle, August 1966, Ph. Bourne and K. Wat tenpaugh, Editors.