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New Solvent Models, Sampling Methods and Maintenance of Amber Software

Amber 软件的新溶剂模型、采样方法和维护

基本信息

批准号：
9974519
负责人：
CARLOS SIMMERLING
金额：
$ 30.42万
依托单位：
STATE UNIVERSITY NEW YORK STONY BROOK
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-08-01 至 2024-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9974519
关键词：
Address Adopted Algorithms Amber Biological Biomedical Computing Code Communities Companions Complex Computer Models Computer Simulation Computer software Consumption DNA Data Development Documentation Evaluation Funding Gene Expression Goals Grain Health Hybrids Industry Informatics Institution Journals Kinetics Lead Maintenance Methodology Methods Modeling Molecular Molecular Computations Molecular Conformation Neck Nucleic Acids Pharmaceutical Preparations Pharmacotherapy Production Productivity Property Protein Engineering Proteins Publishing RNA Folding Resolution Running Sampling Schedule Signal Pathway Signaling Protein Site Small RNA Solvents Source Code Speed Structure System Technology Temperature Testing Thermodynamics Time Variant Water Work aqueous base big-data science design drug discovery experimental study improved kinematics large datasets molecular dynamics nanomaterials programs protein protein interaction screening program simulation tool tutoring virtual screening

项目摘要

Project Summary This proposal responds to PA-14-156, Extended Development, Hardening and Dissemination of Technologies in Biomedical Computing, Informatics and Big Data Science. The goal of this program is to support the continued development, maintenance, testing and evaluation of existing software, matching our proposal. Amber is a very popular software package, used by academic and industry institutions, for simulating the structural, thermodynamic and kinetic properties of molecular systems. The free version of Amber has been downloaded by over 10,000 unique users. There are 3,500 citations to the widely adopted Amber ff99SB protein force field, developed at Stony Brook by PI Carlos Simmerling. The Simmerling group is one of the six academic labs responsible for leading the Amber software maintenance and development effort. Computational molecular dynamics simulations using Amber and other software packages have become essential counterparts to experimental research for understanding the mechanisms of biomolecules, and for discovering drugs to inhibit them. The popular virtual screening program called DOCK interfaces directly with Amber, providing improvements to this widely used program for drug discovery. Other widely used programs also interface with Amber. Productivity in our prior funding period was excellent, leading to articles published in PNAS (2), JACS (3), JCTC (4) and other high-impact journals, with others currently in review. Several new versions of Amber were released. We propose here new developments for Amber, addressing two of the most pressing needs of the field. Aim 1, Solvation: We will incorporate improved solvation models: (a) the SEA semi- explicit water model and (b) a fast but reasonably accurate Generalized Born implicit water model. Aim 2, Sampling: We will add fast and targeted sampling methods: (a) variants of the general tools Hamiltonian exchange and thermal Replica Exchange Molecular Dynamics, (b) the very fast Kinetic-Loop-Closure and Constrained-Loop-Closure methods for sampling loop conformations. Following our practice over the past 20 years, we will openly share our results, parameters and methods, and incorporate them into the Amber production code for distribution with fully documented source code, along with full documentation, test cases, and tutorials. New versions follow an annual release schedule.

项目总结