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Computation & Chemistry Core

计算

基本信息

批准号：
10508446
负责人：
Gregory A. Voth
金额：
$ 79.61万
依托单位：
SEATTLE CHILDREN'S HOSPITAL
依托单位国家：
美国
项目类别：
财政年份：
2022
资助国家：
美国
起止时间：
2022-06-22 至 2027-03-31
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10508446
关键词：
Affinity Area Back Behavior Binding Biological Biological Models Biotinylation Capsid Chemicals Collaborations Communities Complement Computer software Computing Methodologies Data Development Docking Ensure Environment Event Foundations Free Energy Goals Grain HIV HIV-1 Integration Host Factors Kinetics Label Length Life Cycle Stages Machine Learning Mediating Membrane Methodology Methods Modeling Molecular Molecular Conformation Molecular Probes Mutation Nature Nucleic Acids Postdoctoral Fellow Process Proteins Protocols documentation Research Research Personnel Resources Role Sampling Science Site Solvents Speed Structural Models Structure Students Synthesis Chemistry Therapeutic Thermodynamics Time Variant Viral Work base chemical function computational chemistry computer studies computerized tools design fitness inhibitor innovation interest kinetic model models and simulation molecular dynamics molecular modeling multi-scale modeling protein protein interaction rational design simulation small molecule spatiotemporal tool training opportunity virtual virtual screening

项目摘要

ABSTRACT, CORE 1 Core 1 (Voth and Forli, Leads) will provide an extensive and integrated computational capability in support of the science of the B-HIVE Projects. Many processes in HIV-1 that involve proteins, nucleic acids, and/or membranes are inherently multiscale, spanning multiple time and length scales, which vary from the molecular to nanoscopic to mesoscopic. Therefore, in Aim 1 bottom-up multiscale computational methods will be developed and implemented that characterize many-protein assembly processes in the HIV-1 lifecycle. To understand in greater detail the specific physical mechanisms which drive macromolecular interactions of HIV proteins with host factors and nucleic acids, in Aim 2 all-atom molecular dynamics simulations, together with protein-protein docking and kinetic modeling, will be used to build models of HIV proteins interacting with their partners. In order to support the B-HIVE Projects through computational structure-based pipelines and tools for the analysis of targets of interest, Aim 3 will provide well-established computational tools and methods that will also be further developed and extended. All three Aims complement one another and each Aim will provide important input to the other two Aims in an integrated fashion. Overall, Core 1 will extend and develop a set of powerful computational tools in support of the B-HIVE Projects. The Core will also provide valuable new resources for the overall HIV research community and beyond. 1

摘要，核心1 核心1（Voth和福尔利，负责人）将提供广泛的综合计算能力，以支持 B-HIVE项目的科学。HIV-1中涉及蛋白质、核酸和/或膜的许多过程本质上是多尺度的，跨越多个时间和长度尺度，从分子尺度到纳米尺度到介观。因此，在目标1中，将开发自下而上的多尺度计算方法，实现了表征HIV-1生命周期中许多蛋白质组装过程的方法。了解更多详细说明了驱动HIV蛋白与宿主因子的大分子相互作用的特定物理机制和核酸，在Aim 2全原子分子动力学模拟，连同蛋白质-蛋白质对接，动力学建模，将用于建立HIV蛋白与其伴侣相互作用的模型。为了支持 B-HIVE项目通过基于计算结构的管道和工具来分析目标，有趣的是，目标3将提供完善的计算工具和方法，也将进一步发展并延长。所有三个目标相辅相成，每个目标都将为另一个目标提供重要的投入两个目标以一种综合的方式。总的来说，Core 1将扩展和开发一套强大的计算工具，支持B-HIVE项目。该核心还将为艾滋病毒的整体研究提供宝贵的新资源社区和超越。 1