Université Paris Diderot, Sorbonne Paris Cité, Molécules Thérapeutiques In Silico, INSERM UMR-S 973, Paris, France.
INSERM, U973 Paris, France.
Nucleic Acids Res. 2017 Jul 3;45(W1):W350-W355. doi: 10.1093/nar/gkx397.
AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php.
AMMOS2 是一个交互式网络服务器，用于高效计算蛋白质-小分子化合物复合物的精修。AMMOS2 协议采用大量实验或建模的蛋白质-配体复合物的原子水平能量最小化。该网络服务器基于先前开发的独立软件 AMMOS（用于虚拟筛选的自动分子力学优化）。AMMOS 利用基于物理的力场 AMMP sp4，并在蛋白质受体的五个柔韧性水平上对蛋白质-配体相互作用进行优化。在 AMMOS2 网络服务器中实现的新版本 2 允许用户在最小化过程中在蛋白质-配体复合物中包含显式水分子和单个金属离子。该网络服务器提供计算能量的综合分析和精修蛋白质-配体复合物的交互式可视化。根据最小化的结合能对配体进行排序，允许用户对药物发现或化学生物学项目进行额外的分析。该网络服务器已在 21 个不同的蛋白质-配体复合物上进行了广泛测试。AMMOS2 最小化在最小化的蛋白质-配体结合能和水分子位置优化方面显示出对初始复合物结构的一致改进。AMMOS2 网络服务器无需注册即可免费使用，网址为：http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php。
