Classical molecular dynamics and Monte Carlo simulations of protein-drug interactions crucially rely on the parameterisation of atomic interactions through empirical force fields. Although parameters for proteins, water and simple ions are well established, the chemical diversity of drug-like compounds makes it more difficult to generate reliable topologies for these compounds, and specialist knowledge is required for high-quality parameterisations.Ligandbook is a new public database for force-field parameters of small and drug-like molecules. It acts as a repository for high-quality parameter sets, with an initial emphasis on the OPLS-AA force field. In addition to text-based search on compound names, synonyms or abstract words, chemical substructure search allows an easy identification of the desired compounds or functional groups. Parameters are linked to a primary citation in order to support a user in evaluating the quality of the parameter sets.Ligandbook will be available in open access at http://ligandbook.icsn.cnrs-gif.fr.

Ligandbook – an online repository for small and drug-like     molecule force field parameters

244th National Meeting (2012)

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