Computation & Chemistry Core

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

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