The following web utilities, databases and programs can help you in defining and analyzing the interactions between a small molecule (ligand) and the protein.

Interaction Networks of Chemicals and Proteins
open in new window STITCH Search tool for chemical-protein interactions. STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.
   
Databases of Small Molecules in Protein Structures
open in new window HIC-Up
open in new window JenaLib
open in new window Ligand Expo
open in new window MSDchem
open in new window PDB-Ligand
Analysis Tools
open in new window LPC CSU Automated analysis of interatomic contacts between structural units in the protein structure and between the protein and bound ligands.
open in new window MultiBind Multiple alignment of protein binding sites
open in new window PISA Interactive tool for the analysis of macromolecular (protein, DNA/RNA and ligand) interfaces.
open in new window PLATINUM Tool to calculate hydrophobic properties of molecules using the concept of Molecular Hydrophobicity Potential (MHP) and their match or mismatch in receptor–ligand complexes.
Specialized Visualization Tools
open in new window Ligplot
A program to plot schematic diagrams of protein-ligand interactions.
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Binding Sites Comparisons
open in new window MultiBind Multiple alignment of protein binding sites. Recognizes spatial chemical binding patterns common to a set of protein structures
open in new window PESDserv This server allows you to compare surface of lignd bound site against a ligand bound site surface database.
open in new window SiteEngine
3-D alignment of binding sites
open in new window SuMo
SuMo allows you to screen the PDB for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein.