SuperLigands - a database of ligand structures derived from the Protein Data Bank.

ABSTRACT:

Background

Currently, the PDB contains approximately 29,000 protein structures comprising over 70,000 experimentally determined three-dimensional structures of over 5,000 different low molecular weight compounds. Information about these PDB ligands can be very helpful in the field of molecular modelling and prediction, particularly for the prediction of protein binding sites and function.

Description

Here we present an Internet accessible database delivering PDB ligands in the MDL Mol file format which, in contrast to the PDB format, includes information about bond types. Structural similarity of the compounds can be detected by calculation of Tanimoto coefficients and by three-dimensional superposition. Topological similarity of PDB ligands to known drugs can be assessed vi

SUBMITTER: Michalsky E 

PROVIDER: S-EPMC1173082 | biostudies-literature | 2005 May

REPOSITORIES: biostudies-literature