IChem: A Versatile Toolkit for Detecting, Comparing, and Predicting Protein-Ligand Interactions.

Structure-based ligand design requires an exact description of the topology of molecular entities under scrutiny. IChem is a software package that reflects the many contributions of our research group in this area over the last decade. It facilitates and automates many tasks (e.g., ligand/cofactor atom typing, identification of key water molecules) usually left to the modeler's choice. It therefore permits the detection of molecular interactions between two molecules in a very precise and flexible manner. Moreover, IChem enables the conversion of intricate three-dimensional (3D) molecular objects into simple representations (fingerprints, graphs) that facilitate knowledge acquisition at very high throughput. The toolkit is an ideal companion for setting up and performing many structure-based design computations.