I J Bruno | PubMed Health

PubMed1997

Representation and searching of carbohydrate structures using graph-theoretic techniques.

This paper describes how the carbohydrate structures in the Complex Carbohydrate Structure Database (CCSD) can be represented by labelled graphs, in which the nodes and edges of a graph are used to denote the residues and the inter-residue linkages, respectively, of a carbohydrate. These graph representations are then searched with a subgraph-isomorphism algorithm. We describe the use of one such algorithm, that due to Ullmann, and demonstrate that it provides a very precise way of searching the structures in CCSD. We also describe the use of screening techniques that can eliminate many of the CCSD structures from the subgraph-isomorphism search, with a consequent increase in the speed of the search.

Algorithms↗

PubMed1997

IsoStar: a library of information about nonbonded interactions.

Crystallographic and theoretical (ab initio) data on intermolecular nonbonded interactions have been gathered together in a computerised library ('IsoStar'). The library contains information about the nonbonded contacts formed by some 250 chemical groupings. The data can be displayed visually and used to aid protein-ligand docking or the identification of bioisosteric replacements. Data from the library show that there is great variability in the geometrical preferences of different types of hydrogen bonds, although in general there is a tendency for H-bonds to form along lone-pair directions. The H-bond acceptor abilities of oxygen and sulphur atoms are highly dependent on intramolecular environments. The nonbonded contacts formed by many hydrophobic groups show surprisingly strong directional preferences. Many unusual nonbonded interactions are to be found in the library and are of potential value for designing novel biologically active molecules.

Biochemical Phenomena↗