Simulation of Multi-Protein systems
多蛋白系统的模拟
基本信息
- 批准号:10680446
- 负责人:
- 金额:$ 31.08万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2021
- 资助国家:美国
- 起止时间:2021-09-20 至 2025-08-31
- 项目状态:未结题
- 来源:
- 关键词:3-DimensionalAgreementAlgorithmsAlzheimer&aposs disease modelAprotininAreaAwardBindingBiological ModelsBiological ProductsBovine Serum AlbuminCapsidCell physiologyCellsCellular biologyCollaborationsComplexCrowdingDataDevelopmentDiseaseErythrocytesEvaluable DiseaseEvaluationFormulationFourier TransformGoalsGrantHemoglobinImage CompressionLiquid substanceMass Spectrum AnalysisMemoryMethodsMinorModelingMolecular ConformationMultiprotein ComplexesMycoplasma genitaliumNational Institute of General Medical SciencesNucleosome Core ParticlePathway interactionsPeptidesPerformancePharmaceutical PreparationsPropertyProtein ConformationProteinsResolutionRestSamplingSpeedStructureSumSystemValidationVariantWritingexperimental groupexperimental studyflexibilitygamma-Crystallinsimprovedinnovationinsightmethod developmentmolecular assembly/self assemblymolecular modelingmouse modelmulticatalytic endopeptidase complexnovel strategiesparticleprotein aggregationself assemblysimulationtherapeutic development
项目摘要
Simulation of large multi-component molecular assemblies with atomistic details is an important
step toward understanding cellular processes. The goal of this proposal is to develop an
efficient method for the simulation of multi-protein systems consisting of many copies of a few
types of proteins, each in a number of discrete conformations. The basis for our approach is the
observation that the interaction energy between two proteins (or discrete protein conformations
within an ensemble) – can be efficiently calculated over the entire rotational-translational space
using the fast Manifold Fourier transform (FMFT) correlation approach. Given any conformation
of a complex multi-particle system, its energy can be easily obtained by summing the pairwise
interaction energies extracted from the lookup tables. The key innovation to efficiently
implement this method is our ability to compress and store the interaction energy lookup tables
in memory using wavelet sets. We will apply the method in two application. The first is
simulation of multi-protein assemblies and their association pathways, possibly in conjunction
with low resolution Mass Spectrometry (MS) and EM data, providing mechanistic insight into
cellular function. The second is simulation of protein aggregation and crowding, which is
important for the fundamental understanding of cell biology and therapeutic development.
具有原子级细节的多组分分子大组装体的模拟是一个重要的
进一步了解细胞过程。该提案的目标是制定一项
一种有效的方法来模拟多蛋白质系统组成的许多副本的几个
蛋白质的类型,每种都有许多离散的构象。我们方法的基础是
观察到两个蛋白质(或离散蛋白质构象)之间的相互作用能
系综内)-可以在整个旋转-平移空间上有效地计算
使用快速流形傅立叶变换(FMFT)相关方法。考虑到任何形态
一个复杂的多粒子系统,它的能量可以很容易地通过两两相加
从查找表中提取的相互作用能。关键的创新在于
实现这种方法的能力是我们能够压缩和存储相互作用能量查找表
使用小波集保存在内存中。我们将在两个应用程序中应用该方法。一是
模拟多蛋白组装及其关联途径,可能与
利用低分辨率质谱(MS)和EM数据,
细胞功能。第二个是模拟蛋白质聚集和拥挤,
这对细胞生物学和治疗发展的基本理解很重要。
项目成果
期刊论文数量(0)
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科研奖励数量(0)
会议论文数量(0)
专利数量(0)
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Dmytro Kozakov其他文献
Dmytro Kozakov的其他文献
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{{ truncateString('Dmytro Kozakov', 18)}}的其他基金
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ
基于探索多维能量的蛋白质对接细化方法
- 批准号:
8450066 - 财政年份:2010
- 资助金额:
$ 31.08万 - 项目类别:
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ
基于探索多维能量的蛋白质对接细化方法
- 批准号:
8633467 - 财政年份:2010
- 资助金额:
$ 31.08万 - 项目类别:
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ
基于探索多维能量的蛋白质对接细化方法
- 批准号:
8240452 - 财政年份:2010
- 资助金额:
$ 31.08万 - 项目类别:
Refinement Methods for Protein Docking based on Exploring Multi-Dimensional Energ
基于探索多维能量的蛋白质对接细化方法
- 批准号:
8042533 - 财政年份:2010
- 资助金额:
$ 31.08万 - 项目类别:
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