Application of Cloud Computing Resources for Virtual Screening
云计算资源在虚拟放映中的应用
基本信息
- 批准号:8200972
- 负责人:
- 金额:$ 17.01万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2011
- 资助国家:美国
- 起止时间:2011-07-01 至 2013-01-31
- 项目状态:已结题
- 来源:
- 关键词:BackBindingBusinessesChemical StructureComputer SimulationComputer softwareDataDatabasesDevelopmentDiseaseDockingDrug Delivery SystemsDrug IndustryEnvironmentEnzymesEquilibriumEvaluationGoalsHealth Services AccessibilityInternetLearningLibrariesLigandsLinuxModelingMolecular WeightOccupationsOutcomePerformancePhasePreparationProcessProteinsPublic HealthPublishingResearchResearch InfrastructureResearch PersonnelResourcesScheduleScreening ResultScreening procedureSecureServicesSmall Business Innovation Research GrantSoftware ToolsSorting - Cell MovementStructureSystemTechniquesTechnologyTestingTimeLineUniversitiesValidationWorkZincbasecluster computingcomputer infrastructurecomputerized toolscomputing resourcescostcost effectivedrug discoveryhealth economicsimprovedinterestmiddlewarenew technologynovel therapeuticsprogramsreceptorsmall moleculesmall molecule librariessoftware developmenttherapeutic targettooltool developmentvirtualweb interfaceweb services
项目摘要
DESCRIPTION (provided by applicant): This is an application to develop a scalable computational infrastructure to enable virtual screening of chemical libraries using the Amazon EC2 cloud computing environment and automated docking tools. Structure-based virtual screening is an important tool in the drug discovery process (1-7). The use of computational tools has allowed for the screening of large libraries of chemical compounds to identify putative ligand-receptor interactions (8-9). The identification of valid targets and therapeutic compounds has long-term importance both to the public health and the economic strength of the pharmaceutical industry. Receptor-based virtual screening (VS) is a technique in which computational tools are used dock small molecular weight compounds into a protein receptor or enzyme. This technique is most often used in drug discovery, where a large library of chemical structure can be docked and scored to assess the potential if a compound to bind to a drug target. However, high-throughput virtual screening is computationally intensive, and the cost of building, maintaining, and managing a dedicated computing cluster limits access to these technologies to large universities and commercial enterprises. Internet-based computing, also known as cloud computing, is a business service model in which computational resources are accessed on-demand as needed, and is affordable, scalable, and secure. We have utilized the Amazon EC2 cloud computing environment for virtual screening of chemical libraries of 100 to 10000 compounds against two targets of therapeutic interest. This application will further expand the capacity for virtual screening by: (1) development of the software infrastructure required for computational cluster virtualization and management; (2) development of a basic user interface for submission and management of virtual screening requests and evaluation of results; (3) validation of this approach through analysis of screening results with our collaborators. The test of this platform will be focused on function and utility: (1) demonstrate the ability to screen a library of 1.4 million to 2.0 million compounds against known therapeutic targets; (2) comparison of performance against a dedicated cluster using equivalent docking software, chemical libraries, and targets; (3) ability to utilize the web interface to conduct virtual screens.
PUBLIC HEALTH RELEVANCE: The Phase I SBIR project "Application of Cloud Computing Resources for Virtual Screening" will deliver new technologies for the structure-based identification of small molecule ligands of proteins and enzymes. By significantly increasing the ability of researchers to access tools for in-silico screening, we will facilitate identification of novel therapeutic compounds used in the treatment of disease, and thereby improving the public health.
描述(由申请人提供):这是一个应用程序,旨在开发可扩展的计算基础设施,以使用Amazon EC2云计算环境和自动对接工具实现对化学库的虚拟筛选。基于结构的虚拟筛选是药物发现过程中的重要工具(1-7)。计算机工具的使用使得能够筛选大型化合物库以确定假定的配体-受体相互作用(8-9)。有效靶点和治疗化合物的确定对公众健康和制药业的经济实力都具有长期的重要性。基于受体的虚拟筛选(VS)是一种使用计算工具将小分子化合物对接到蛋白质受体或酶中的技术。这项技术最常用于药物发现,可以对接和评分大型化学结构库,以评估化合物是否与药物靶点结合的可能性。然而,高吞吐量虚拟筛选需要大量计算,而且构建、维护和管理专用计算集群的成本限制了大型大学和商业企业对这些技术的使用。基于互联网的计算,也称为云计算,是一种商业服务模式,在这种模式下,计算资源可以根据需要按需访问,并且价格合理、可扩展且安全。我们已经利用AmazonEC2云计算环境针对两个治疗目标虚拟筛选了100到10000个化合物的化学库。该应用程序将通过以下方式进一步扩大虚拟筛选的能力:(1)开发计算集群虚拟化和管理所需的软件基础设施;(2)开发用于提交和管理虚拟筛选请求和评估结果的基本用户界面;(3)通过与我们的合作者分析筛选结果来验证这一方法。该平台的测试将集中在功能和实用性上:(1)展示针对已知治疗靶点筛选140万至200万化合物库的能力;(2)使用同等的对接软件、化学库和靶标与专用群集进行性能比较;(3)利用网络界面进行虚拟筛选的能力。
与公众健康相关:SBIR第一阶段项目“云计算资源在虚拟筛选中的应用”将提供基于结构的蛋白质和酶小分子配体识别的新技术。通过显著提高研究人员获得硅内筛查工具的能力,我们将促进识别用于疾病治疗的新型治疗化合物,从而改善公众健康。
项目成果
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