Chembench: the Integrated Web Portal to Accelerate Cheminformatics and Chemical G

Chembench：加速化学信息学和化学 G 发展的综合门户网站

• 批准号: 8727051
• 负责人: Diane Pozefsky
• 金额: $ 28.88万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8727051
• 关键词: Address; Architecture; Area; Benchmarking; Bioinformatics; Biological; Biological Models; Biological Sciences; Biological databases; Biology; Biomedical Research; Chemical Structure; Chemicals; Chemistry; Collection; Computer Analysis; Computer software; Data; Data Analyses; Data Quality; Data Set; Databases; Descriptor; Discipline; Elements; Ensure; Environment; Generations; Generic Drugs; Genomics; Grant; Imagery; Individual; Informatics; Institution; Internet; Knowledge; Knowledge Discovery; Laboratories; Libraries; Licensing; Literature; Medicine; Methodology; Modeling; Molecular Models; National Human Genome Research Institute; National Institute of Drug Abuse; National Institute of Environmental Health Sciences; National Institute of General Medical Sciences; National Institute of Mental Health; Nature; Play; Preparation; Procedures; Process; Property; Protocols documentation; Public Domains; Public Health; Quantitative Structure-Activity Relationship; Research; Research Infrastructure; Research Personnel; Research Support; Retrieval; Role; Running; Sampling; Scientist; Services; Software Design; Structure; System; Techniques; TimeLine; Toxic effect; Translating; United States National Institutes of Health; Update; Validation; abstracting; base; biological research; chemical property; cheminformatics; compare effectiveness; computer framework; computer infrastructure; computerized tools; data mining; data modeling; design; drug candidate; drug discovery; high throughput technology; improved; interest; model development; molecular modeling; novel; predictive modeling; research study; screening; small molecule libraries; statistics; tool; virtual

DESCRIPTION (provided by applicant): ChemBench: the Integrated Web Portal to Accelerate Cheminformatics and Chemical Genomics Research. Project Summary/Abstract As a result of growing proliferation of high-throughput technologies in modern chemical and biological research, the experimental scientists generating large volumes of data are no longer equipped with adequate tools and approaches to manage, let alone analyze, their own data. Modern chemical and biological research requires sophisticated public-domain tools for computational and statistical analysis of large experimental datasets to create data models that can aid and prioritize further experiments. Cheminformatics has emerged in the last decade as a burgeoning research discipline combining computational, statistical, and informational methodologies with some of the key concepts in chemistry and biology. Modern cheminformatics is defined broadly as a chemocentric scientific discipline encompassing the creation, retrieval, management, visualization, modeling, discovery, and dissemination of chemical knowledge. Further progress of cheminformatics research is hampered by the lack of publicly available computational tools and software to analyze chemical genomics data. This project endeavors to fill this gap through an advanced cheminformatics web portal called Chembench. The current system has been built in our group in the last four years with limited initial support from the NIH RoadMap planning grant. This project will advance Chembench to become an easily extensible and maintainable system addressing the needs of both computational and experimental chemical genomics scientists by providing a freely available model building tool for cheminformaticians and freely available compound activity predicting tools for biologists and medicinal chemists. The computational workflow to incorporate these key procedures and afford their transparent use must be based on rigorous software design approaches and procedures that constitute the focus of Specific Aim 1 of this project. Building upon this rigorous computational infrastructure, the functional key elements of the workflow include modules for (i) chemical data preparation including curation, descriptor calculation, and chemical space visualization (Aim 2); (ii) QSAR model development and statistical validation (Aim 3); (iii) prediction of computational hits in external compound libraries (Aim 4); and (iv) analysis and exploration of computational hits (Aim 5). The portal is designed as an aggregate of modules that can be used as part of an automated integrated workflow or individually, depending on the research interests and specific expertise of users. Similar to the role that bioinformatics has played in transforming modern biomedical research; cheminformatics is poised to revolutionize all areas of research in chemistry and chemical biology. Chembench provides the experimental and computational probe/drug discovery researchers with knowledge discovery tools and infrastructure that enables them to explore and exploit chemical genomics databases, build rigorous data models, and reduce the experimental effort required to identify novel biologically active compounds. The publicly available Chembench portal will help translate large scale chemical genomics research into the discovery of new medicines to improve public health.

描述（由申请人提供）：Chembench：综合Web门户，以加速化学信息和化学基因组学研究。由于现代化学和生物学研究中高通量技术的扩散越来越大，生成大量数据的实验科学家不再配备了足够的工具和方法来管理自己的数据，因此，由于现代化学和生物学研究中的高通量技术的扩散越来越大，更不用说分析自己的数据。现代化学和生物学研究需要大型实验数据集的计算和统计分析的复杂公共域工具，以创建可以帮助和优先级进一步实验的数据模型。在过去的十年中，化学信息学已成为一项新兴的研究学科，将计算，统计和信息方法与化学和生物学中的一些关键概念相结合。现代化学信息学广泛定义为一种化学中心科学学科，其中包括创造，检索，管理，可视化，建模，发现和化学知识的传播。由于缺乏公开可用的计算工具和软件来分析化学基因组学数据，化学信息学研究的进一步进展受到了阻碍。该项目努力通过称为ChemBench的高级化学信息网络门户来填补这一空白。在过去的四年中，当前的系统是在我们的小组中建造的，而NIH路线图计划赠款的初步支持有限。该项目将使Chembench成为一个易于扩展和可维护的系统，通过为化学物质医生提供免费可用的模型构建工具，并为生物学家和药物化学家提供预测工具，以满足计算和实验化学基因组学科学家的需求。合并这些关键程序及其透明使用的计算工作流程必须基于严格的软件设计方法和过程，构成了该项目的特定目标1的重点。在这种严格的计算基础架构的基础上，工作流的功能关键要素包括（i）化学数据制备的模块，包括策展，描述符计算和化学空间可视化（AIM 2）； （ii）QSAR模型开发和统计验证（AIM 3）； （iii）预测外部化合物库中的计算打击（AIM 4）； （iv）计算命中的分析和探索（AIM 5）。该门户被设计为模块的汇总，可以用作自动化集成工作流的一部分或单独使用，具体取决于用户的研究兴趣和特定专业知识。类似于生物信息学在改变现代生物医学研究中的作用；化学信息学有望彻底改变化学和化学生物学研究的所有研究领域。 Chembench为实验和计算探针/药物发现研究人员提供了知识发现工具和基础架构，使他们能够探索和利用化学基因组学数据库，建立严格的数据模型并减少识别新型生物学活性化合物所需的实验努力。公开可用的Chembench门户将有助于将大规模的化学基因组学研究转化为发现新药物以改善公共卫生。