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

基本信息

批准号：
8258998
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
项目类别：
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/8258998
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 Screening procedure 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 small molecule libraries statistics tool virtual

项目摘要

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. PUBLIC HEALTH RELEVANCE: This project intends to develop a publicly available cheminformatics ChemBench portal to provide the experimental and computational probe/drug discovery researchers with knowledge discovery tools and infrastructure to explore and exploit chemical genomics databases, build rigorous data models, and reduce the amount of experimental effort required to identify novel biologically active compounds such as chemical probes and drug candidates.

描述（由申请人提供）：ChemBench：加速化学信息学和化学基因组学研究的综合门户网站。项目摘要/摘要由于现代化学和生物研究中高通量技术的不断普及，生成大量数据的实验科学家不再配备足够的工具和方法来管理（更不用说分析）自己的数据了。现代化学和生物研究需要复杂的公共领域工具来对大型实验数据集进行计算和统计分析，以创建可以帮助和优先考虑进一步实验的数据模型。化学信息学在过去十年中作为一门新兴的研究学科出现，它将计算、统计和信息方法与化学和生物学的一些关键概念相结合。现代化学信息学被广泛定义为一门以化学为中心的科学学科，涵盖化学知识的创建、检索、管理、可视化、建模、发现和传播。由于缺乏公开可用的计算工具和软件来分析化学基因组数据，化学信息学研究的进一步进展受到阻碍。该项目致力于通过名为 Chembench 的先进化学信息学门户网站来填补这一空白。目前的系统是我们小组在过去四年中建立的，并得到了 NIH 路线图规划拨款的有限初步支持。该项目将通过为化学信息学家提供免费的模型构建工具，为生物学家和药物化学家提供免费的化合物活性预测工具，将推动 Chembench 成为一个易于扩展和维护的系统，满足计算和实验化学基因组学科学家的需求。纳入这些关键程序并提供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程序，这些方法和程序构成了该项目具体目标 1 的重点。建立在这种严格的计算基础设施之上，工作流程的功能关键要素包括以下模块：(i) 化学数据准备，包括管理、描述符计算和化学空间可视化（目标 2）； (ii) QSAR 模型开发和统计验证（目标 3）； (iii) 预测外部化合物库中的计算命中（目标 4）； (iv) 计算命中的分析和探索（目标 5）。该门户被设计为模块的集合，这些模块可以用作自动化集成工作流程的一部分，也可以单独使用，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所发挥的作用；化学信息学有望彻底改变化学和化学生物学的所有研究领域。 Chembench 为实验和计算探针/药物发现研究人员提供知识发现工具和基础设施，使他们能够探索和利用化学基因组数据库、建立严格的数据模型并减少识别新型生物活性化合物所需的实验工作。公开的 Chembench 门户将有助于将大规模化学基因组学研究转化为新药的发现，以改善公众健康。公共健康相关性：该项目旨在开发一个公开的化学信息学 ChemBench 门户，为实验和计算探针/药物发现研究人员提供知识发现工具和基础设施，以探索和利用化学基因组数据库，建立严格的数据模型，并减少鉴定新型生物活性化合物（例如化学探针和候选药物）所需的实验工作。