LS-align: an atom-level, flexible ligand structural alignment algorithm for high-throughput virtual screening

Jun Hu, Zi Liu, Dong-Jun Yu, Yang Zhang

Abstract: Sequence-order independent structural comparison, also called structural alignment, of small ligand molecules is often needed for computer-aided virtual drug screening. Although many ligand structure alignment programs are proposed, most of them build the alignments based on rigid-body shape comparison which cannot provide atom-specific alignment information nor allow structural variation; both abilities are critical to efficient high-throughput virtual screening.