Parameter relation rows: a query system for protein structure function relationships.
In the course of molecular modeling or mutant prediction one often wants quick answers to questions such as: 'Are there any residues in a beta-strand that point into an internal cavity, and are highly mutable?' 'Are there large polar residues in a helix that make a contact with a hydrophobic residue in a sheet, and don't make the maximal number of hydrogen bonds?' or 'Which hydrophobic residues are in a helix with a large hydrophobic moment, and make a contact with a co-factor, but at the same time still have a large accessible surface?'. I describe here a method to get answers to these kinds of questions in a very quick and easy manner. The method described is partly based on the principles used in the design of relational databases, and its mode of operation is similar to the query methods used in a relational database environment. Although designed for aiding in molecular modeling, its applicability is much more general. The method has been implemented as part of a large molecular modeling package which copes with the numerous problems in 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.
Vriend
G
G
Department of Biocomputing, EMBL, Heidelberg, FRG.
D016208:Databases, Factual; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013329:Structure-Activity Relationship
D011506:Proteins