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

• 批准号: 8888032
• 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
• 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/8888032
• 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; 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; models and simulation; novel strategies; open source; particle; programs; protein folding; protein misfolding; protein structure prediction; public health relevance; research study; response; screening; simulation; solute; tool

 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.