title: ALFA: automatic ligand flexibility assignment.
abstract: 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.
authors.affiliation: Unidad de Bioinformática, Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Campus de Cantoblanco UAM , E-28049 Madrid, Spain.
authors.forename: Javier
authors.initials: J
authors.lastname: Klett
authors.forename: Álvaro
authors.initials: Á
authors.lastname: Cortés-Cabrera
authors.forename: Rubén
authors.initials: R
authors.lastname: Gil-Redondo
authors.forename: Federico
authors.initials: F
authors.lastname: Gago
authors.forename: Antonio
authors.initials: A
authors.lastname: Morreale
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D057166:High-Throughput Screening Assays; D008024:Ligands; D008968:Molecular Conformation; D012984:Software; D055672:Static Electricity; D014584:User-Computer Interface
chemical_list: D008024:Ligands