Pencheva T, Lagorce D, Pajeva I, Villoutreix B O, Miteva M A
Institute of Biophysics and Biomedical Engineering, Bulgarian Academy of Sciences, Sofia, Bulgaria.
Methods Mol Biol. 2012;819:127-41. doi: 10.1007/978-1-61779-465-0_9.
Recent advances in computational sciences enabled extensive use of in silico methods in projects at the interface between chemistry and biology. Among them virtual ligand screening, a modern set of approaches, facilitates hit identification and lead optimization in drug discovery programs. Most of these approaches require the preparation of the libraries containing small organic molecules to be screened or a refinement of the virtual screening results. Here we present an overview of the open source AMMOS software, which is a platform performing an automatic procedure that allows for a structural generation and optimization of drug-like molecules in compound collections, as well as a structural refinement of protein-ligand complexes to assist in silico screening exercises.
计算科学的最新进展使得在化学与生物学交叉领域的项目中能够广泛使用计算机模拟方法。其中，虚拟配体筛选作为一套现代方法，有助于在药物发现项目中识别活性化合物并进行先导化合物优化。这些方法大多需要制备包含待筛选的有机小分子的文库，或者对虚拟筛选结果进行优化。在此，我们概述了开源的AMMOS软件，它是一个执行自动程序的平台，可在化合物库中生成并优化类药物分子的结构，还能对蛋白质-配体复合物进行结构优化，以辅助计算机模拟筛选工作。
