AMBER/PBSA: An Open-Source Computer Program for Accurate and Scalable Solvation Analysis ofBiomolecules

 描述(由申请人提供)：生物分子的原子模拟提供了补充实验的结构和动力学的详细视图。在新算法和计算机能力增长的推动下，构象采样增加，现在可以观察到更广泛的事件，提供了关键的洞察力，这在很大程度上是实验无法获得的。隐式溶剂化处理的进展使模拟进一步扩展到更广泛的生物分子结构、动力学和功能的研究，包括蛋白质折叠和错误折叠、蛋白质结构预测、蛋白质与配体结合、酶机制和药物设计。Amber/PBSA程序是一个开源的计算机程序，用于生物分子的隐式溶剂化建模。在这个项目中，我们建议继续维护和改进Amber/PBSA程序，方法是：(1)根据用户的建议发展和改进Amber/PBSA程序；(2)开发和集成轻量级分析工具，以促进更好的分子模拟；(3)开发没有明显溶剂/溶质界面的复杂体系的介电模型；以及(4)继续验证PB模型。

 DESCRIPTION (provided by applicant): Atomistic simulations of biomolecules provide a detailed view of structure and dynamics that complement experiments. Increased conformational sampling, enabled by new algorithms and growth in computer power, now allows a much broader range of events to be observed, providing critical insights, largely inaccessible to experiments. Advancements in implicit solvation treatments have furthered the simulation reach to a broader range of studies of biomolecular structure, dynamics and function, including protein folding and misfolding, protein structure prediction, protein-ligand binding, enzyme mechanisms, and drug design. The AMBER/PBSA program is an open-source computer program for implicit solvation modeling of biomolecules. In this project, we propose to continue the maintenance and improvement of the AMBER/PBSA program by (1) growing and improving the AMBER/PBSA program in response to suggestions by our users; (2) developing and integrating lightweight analysis tools to facilitate better molecular simulations; (3) developing dielectric model for complex systems without apparent solvent/solute interface; and (4) continuing to validate the PB models.