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。通过新算法和计算机能力的增长，构象采样的增加现在允许观察更广泛的事件，提供实验无法获得的重要见解。隐式溶剂化处理的进步将模拟扩展到更广泛的生物分子结构、动力学和功能研究，包括蛋白质折叠和错误折叠、蛋白质结构预测、蛋白质-配体结合、酶机制和药物设计。 AMBER/PBSA 程序是一个用于生物分子隐式溶剂化建模的开源计算机程序。在本项目中，我们建议通过以下方式继续维护和改进 AMBER/PBSA 程序：（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/溶质界面的复杂系统的介电模型； (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.