Parameter relation rows: a query system for protein structure function relationships

In the course of molecular modeling or mutant prediction oneoften wants quick answers to questions such as: ‘Are thereany residues in a beta-strand that point into an internal cavity,and are highly mutable?;’ ‘Are there large polarresidues in a helix that make a contact with a hydrophobic residuein a sheet, and don't make the maximal number of hydrogen bonds?’or ‘Which hydrophobic residues are in a helix with a largehydrophobic moment, and make a contact with a co-factor, butat the same time still have a large accessible surface?’.I describe here a method to get answers to these kinds of questionsin a very quick and easy manner. The method described is partlybased on the principles used in the design of relational databases,and its mode of operation is similar to the query methods usedin a relational database environment. Although designed foraiding in molecular modeling, its applicability is much moregeneral. The method has been implemented as part of a largemolecular modeling package which copes with the numerous problemsin systematic handling of protein structures, e.g. residue numbering.This also implies that many normal tools such as graphical analyses,I/O facilities, etc. are available on-line.