Lead optimization mapper: automating free energy calculations for lead optimization.

ABSTRACT: Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained bet

SUBMITTER: Liu S 

PROVIDER: S-EPMC3837551 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature