PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures - PubMed (original) (raw)

PDB-Ligand: a ligand database based on PDB for the automated and customized classification of ligand-binding structures

Jae-Min Shin et al. Nucleic Acids Res. 2005.

Abstract

PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structures. As of May 2004, there are about 4870 types of small molecular ligands, experimentally determined as a complex with protein or DNA in the PDB. The proteins that a given ligand binds are often homologous and present the same binding structure to the ligand. However, there are also many instances wherein a given ligand binds to two or more unrelated proteins, or to the same or homologous protein in different binding environments. PDB-Ligand serves as an interactive structural analysis and clustering tool for all the ligand-binding structures in the PDB. PDB-Ligand also provides an easier way to obtain a number of different structure alignments of many related ligand-binding structures based on a simple and flexible ligand clustering method. PDB-Ligand will be a good resource for both a better interpretation of ligand-binding structures and the development of better scoring functions to be used in many drug discovery applications.

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Figures

Figure 1

Figure 1

Scheme used in the PDB-Ligand database construction.

Figure 2

Figure 2

A typical ATP-ligand cluster, obtained using default options. The 10 ATP-binding structures from 10 PDB entries are displayed in the ligand-information table on the left-hand side. The superimposed ATP-binding structures are shown in the chime-window in stereo view. ATP is shown in CPK model and the surrounding amino acids as connected line segments in different colors depending on the residue type. The chime utilities were used for the graphics rendering.

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