10.1021/ci400453n.s002 Javier Klett Javier Klett Álvaro Cortés-Cabrera Álvaro Cortés-Cabrera Rubén Gil-Redondo Rubén Gil-Redondo Federico Gago Federico Gago Antonio Morreale Antonio Morreale ALFA: Automatic Ligand Flexibility Assignment American Chemical Society 2014 screening protocols ligand flexibility user interface graphics program PyMOL nonexpert users molecule Automatic Ligand Flexibility AssignmentALFA iterative algorithm representative conformers 2014-01-27 00:00:00 Journal contribution https://acs.figshare.com/articles/journal_contribution/ALFA_Automatic_Ligand_Flexibility_Assignment/2329267 ALFA is a fast computational tool for the conformational analysis of small molecules that uses a custom-made iterative algorithm to provide a set of representative conformers in an attempt to reproduce the diversity of states in which small molecules can exist, either isolated in solution or bound to a target. The results shown in this work prove that ALFA is fast enough to be integrated into massive high-throughput virtual screening protocols with the aim of incorporating ligand flexibility and also that ALFA reproduces crystallographic X-ray structures of bound ligands with great accuracy. Furthermore, the application includes a graphical user interface that allows its use through the popular molecular graphics program PyMOL to make it accessible to nonexpert users. ALFA is distributed free of charge upon request from the authors.