title: Flexible alignment of small molecules using the penalty method.
abstract: An efficient flexible alignment method using the penalty method, called FAP, is described. FAP is a pairwise alignment algorithm that matches a flexible sample to a rigid template. It is a pure atom-based 3D method that utilizes the modified SEAL similarity index combined with an energy penalty term. The penalty term, defined as the third power of the ratio of the local strain energy to its target value, enables effective control of energy increase during alignment. The alignment procedure consists of the seed conformer generation, rigid-body alignment, and flexible optimization steps. Both conformation and alignment spaces are efficiently explored by the sparse, random sampling schemes. FAP has been tested with benchmark sets of seven different classes of ligands taken from the literature. In terms of the ability to produce the bioactive overlays, FAP is comparable to, or in some cases better than, other alignment methods. FAP is accurate, objective, fully automated, and fast enough to be used as a tool for virtual screening.
authors: Department of Chemistry and Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Korea. nswcshin@plaza.snu.ac.kr
authors: Whanchul
authors: W
authors: Shin
authors: Seung Ah
authors: SA
authors: Hyun
authors: Chong Hak
authors: CH
authors: Chae
authors: Jae Kyung
authors: JK
authors: Chon
mesh_terms: D000465:Algorithms; D015195:Drug Design; D008958:Models, Molecular; D008968:Molecular Conformation; D054852:Small Molecule Libraries / Q000737:chemistry*
chemical_list: D054852:Small Molecule Libraries