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

AMBER/PBSA：用于精确且可扩展的生物分子溶剂化分析的开源计算机程序

基本信息

批准号：
9015448
负责人：
RAY LUO
金额：
$ 28.73万
依托单位：
UNIVERSITY OF CALIFORNIA-IRVINE
依托单位国家：
美国
项目类别：
财政年份：
2010
资助国家：
美国
起止时间：
2010-05-01 至 2019-01-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9015448
关键词：
Adopted Algorithms Benchmarking Binding Proteins Biomedical Research Charge Communities Comparative Study Complement Complex Computer software Computers Data Development Drug Design Electrostatics Ensure Equation Equilibrium Evaluation Event Experimental Models Grant Growth Health Imagery Investigation Ions Ligands Maintenance Measurement Membrane Methods Modeling Molecular Nucleic Acid Folding Nucleic Acids Performance Play Positioning Attribute Proteins Protocols documentation Publications Research Personnel Role Sampling Science Solvents Structure Suggestion Surface System Translational Research Universities Validation Work base computer program drug discovery enzyme mechanism improved insight interest light weight models and simulation novel strategies open source particle programs protein folding protein misfolding protein structure prediction research study response screening simulation solute tool

项目摘要

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.

描述（由应用程序提供）：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。现在，通过新算法和计算机功率增长来实现构象采样的增加，现在可以观察到更广泛的事件，从而提供了关键的见解，这在很大程度上无法获得实验。隐式溶液处理中的进步已将模拟范围进一步延伸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 - 配体结合，酶机制和药物设计。 Amber/PBSA程序是一种开源计算机程序，用于隐式解决方案模型。在这个项目中，我们建议通过（1）以（1）对用户的建议进行增长和改进琥珀/PBSA计划来继续维护和改善琥珀/PBSA计划；（2）开发和集成轻量分析工具，以促进更好的分子模拟；（3）开发不具有明显溶剂/溶质界面的复杂系统的饮食模型；（4）继续验证PB模型。