ALFA: Automatic Ligand Flexibility Assignment

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.