Computer Simulations of Protein Structure and Dynamics

蛋白质结构和动力学的计算机模拟

基本信息

批准号：
7932626
负责人：
Ronald Levy
金额：
$ 14.53万
依托单位：
RUTGERS, THE STATE UNIV OF N.J.
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2011-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7932626
关键词：
Acceleration Accounting Address Adopted Algorithms Arts Attention Back Binding Binding Proteins Biophysics Collaborations Communication Communities Complement Complex Computer Hardware Computer Simulation Computers Crystallography Cytochromes Data Set Databases Development Disease Pathway Drug Design Electrostatics Engineering Environment Equation Equilibrium Experimental Models Foundations Free Energy Freedom Goals Grant HIV-1 High temperature of physical object Hydration status Investigation Kinetics Laboratories Language Lead Ligand Binding Ligands Link Linux Literature Manuscripts Methodology Methods Modeling Molecular Molecular Conformation Nature Paper Pathway interactions Peptides Physical Chemistry Population Potential Energy Preparation Process Property Proteins Reaction Recording of previous events Research Resolution Ribonuclease H Running Sampling Simulate Solutions Solvents Specificity Staging Statistical Mechanics Structure Surface System Techniques Temperature Testing Thermodynamics Thinking Time Validation Walking Work alpha synuclein base cold temperature data exchange experience flexibility improved inhibitor/antagonist insight interest migration molecular dynamics molecular mechanics network models novel polypeptide protein complex protein folding protein structure receptor research and development research study simulation structural biology tool

项目摘要

DESCRIPTION (provided by applicant): The goals of this research are the development of more accurate methods for molecular simulations of solvated proteins, and their application to forefront problems in structural biology and molecular biophysics. There are three specific aims of this proposal: (1) continue to improve detailed atomic models with implicit solvent for biomolecular simulations, (2) develop advanced sampling methods for biomolecular simulations based on novel implementations of replica exchange, and (3) apply these state-of-the-art effective potentials and sampling methods to key problems in structural biology: (a) ligand binding to proteins, (b) characterization of polypeptide structural ensembles and folding pathways, and (c) modeling of crystalline vs. solution environment effects on proteins at high resolution. These projects will build on the substantial progress made during the current grant period in the development of state-of-the-art effective potentials and novel sampling methods for protein simulations, and forefront applications which are best suited to investigation using all atom models.

描述（由申请人提供）：这项研究的目标是开发更准确的溶剂化蛋白分子模拟方法，以及它们在结构生物学和分子生物物理学中的最前沿问题中的应用。该提案有三个具体目的：（1）继续改善具有隐式溶剂的生物分子模拟的详细原子模型，（2）开发基于复制品交换的新实现的生物分子模拟的先进采样方法，（3）将这些先进的有效潜力和取样方法应用于结构性生物学的键入：（A），（3）多肽结构集合和折叠途径，以及（c）晶体与溶液环境对蛋白质的影响对蛋白质高分辨率的影响。这些项目将建立在当前赠款期间在开发最新有效潜力和蛋白质模拟的新型抽样方法的基础上，以及最适合使用所有原子模型进行调查的最前沿应用。