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

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

项目成果

期刊论文数量(9)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Accelerating the Ensemble Convergence of RNA Hairpin Simulations with a Replica Exchange Structure Reservoir.
  • DOI:
    10.1021/acs.jctc.2c00065
  • 发表时间:
    2022-05
  • 期刊:
  • 影响因子:
    5.5
  • 作者:
    Kenneth Lam;Koushik Kasavajhala;Sarah Gunasekera;Carlos Simmerling
  • 通讯作者:
    Kenneth Lam;Koushik Kasavajhala;Sarah Gunasekera;Carlos Simmerling
Fast Pairwise Approximation of Solvent Accessible Surface Area for Implicit Solvent Simulations of Proteins on CPUs and GPUs.
Exploring Protocols to Build Reservoirs to Accelerate Temperature Replica Exchange MD Simulations.
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CARLOS SIMMERLING其他文献

CARLOS SIMMERLING的其他文献

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{{ truncateString('CARLOS SIMMERLING', 18)}}的其他基金

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
  • 批准号:
    8870395
  • 财政年份:
    2013
  • 资助金额:
    $ 30.42万
  • 项目类别:
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
  • 批准号:
    8558811
  • 财政年份:
    2013
  • 资助金额:
    $ 30.42万
  • 项目类别:
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
  • 批准号:
    8708162
  • 财政年份:
    2013
  • 资助金额:
    $ 30.42万
  • 项目类别:
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
  • 批准号:
    9091615
  • 财政年份:
    2013
  • 资助金额:
    $ 30.42万
  • 项目类别:
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
  • 批准号:
    9447617
  • 财政年份:
    2013
  • 资助金额:
    $ 30.42万
  • 项目类别:
IMPROVING BIOMOLECULAR SIMULATIONS: ENERGY FUNCTIONS AND CONFORMATIONAL SAMPLIN
改进生物分子模拟:能量函数和构象采样
  • 批准号:
    7601279
  • 财政年份:
    2007
  • 资助金额:
    $ 30.42万
  • 项目类别:
IMPROVING BIOMOLECULAR SIMULATIONS: ENERGY FUNCTIONS AND CONFORMATIONAL SAMPLIN
改进生物分子模拟:能量函数和构象采样
  • 批准号:
    7181633
  • 财政年份:
    2004
  • 资助金额:
    $ 30.42万
  • 项目类别:
Improving Biomolecular Simulations: Energy Functions and Conformational Samplin
改进生物分子模拟:能量函数和构象采样
  • 批准号:
    6980073
  • 财政年份:
    2004
  • 资助金额:
    $ 30.42万
  • 项目类别:
ENHANCED MEAN-FIELD SIMULATIONS OF ANTIBODY CDR LOOPS
抗体 CDR 环的增强平均场模拟
  • 批准号:
    6387206
  • 财政年份:
    2000
  • 资助金额:
    $ 30.42万
  • 项目类别:
Computational Studies of Model Systems for Protein Unfolded States
蛋白质未折叠状态模型系统的计算研究
  • 批准号:
    7095359
  • 财政年份:
    2000
  • 资助金额:
    $ 30.42万
  • 项目类别:

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