SuperLigands – a database of ligand structures derived from the Protein Data BankReport as inadecuate




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BMC Bioinformatics

, 6:122

First Online: 19 May 2005Received: 03 February 2005Accepted: 19 May 2005

Abstract

BackgroundCurrently, 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.

DescriptionHere 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 via Tanimoto coefficients.

ConclusionSuperLigands supplements the set of existing resources of information about small molecules bound to PDB structures. Allowing for three-dimensional comparison of the compounds as a novel feature, this database represents a valuable means of analysis and prediction in the field of biological and medical research.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-6-122 contains supplementary material, which is available to authorized users.

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Author: Elke Michalsky - Mathias Dunkel - Andrean Goede - Robert Preissner

Source: https://link.springer.com/







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