Author: Kenneth Longo
The cheminformatics world is replete with software tools and file formats for the design, manipulation and management of small molecules and libraries thereof. Those tools and formats are often specialized in analyzing small molecules of ~500 daltons, give or take a few, or those molecules that can reasonably be drawn and understood using classic ball-and-stick or molecular coordinate frameworks. Perhaps not coincidentally, this neatly envelops the needs of small molecule drug discovery, where it is not uncommon to find both public and privately-held repositories of hundreds of thousands (to millions) of such molecules, for use in molecular or phenotypic screening assays. The small size and elemental simplicity of these molecules has resulted in a variety of storage file formats (e.g., mol, SMILES, sdf, etc) and many supporting software packages (e.g., RDkit, CDK, ChemAxon, etc) for visualization and manipulation that support them. KNIME Analytics Platform provides easy access to those file formats and software packages.