RBVI OUTREACH AND TRAINING

RBVI 外展和培训

• 批准号: 8363626
• 负责人: THOMAS E FERRIN
• 金额: $ 10.94万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-07-01 至 2012-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8363626
• 关键词: Active Sites; Amino Acid Sequence; Automobile Driving; Awareness; Bioinformatics; Biological; Chimera organism; Communities; Computational algorithm; Computer software; Consult; Data; Data Analyses; Databases; Development; Education and Outreach; Educational process of instructing; Electrostatics; Enzymes; Funding; Grant; Image; Imagery; Informatics; Link; Maps; Metabolic Pathway; Methods; Molecular; Molecular Biology; Molecular Models; National Center for Research Resources; Pathway Analysis; Peptide Sequence Determination; Pharmaceutical Preparations; Principal Investigator; Protein Engineering; Publications; Reaction; Research; Research Infrastructure; Resource Development; Resources; Sequence Alignment; Sequence Analysis; Services; Software Tools; Source; Structure; System; United States National Institutes of Health; base; biocomputing; chemical reaction; cost; electron density; innovation; interest; member; molecular modeling; movie; open source; protein structure; small molecule; structural biology; tool

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The Resource for Biocomputing, Visualization and Informatics (RBVI) develops innovative methods and algorithms for computational and visualization-based data analysis, implements these as professional-quality, easy-to-use software tools, and applies the tools toward solving a wide range of problems relating to molecular sequence, structure, and function. UCSF Chimera (www.cgl.ucsf.edu/chimera) is the molecular modeling package under active development by the RBVI. Chimera is a tool for visualization and analysis of biomolecular structures and interactions. In addition to atomic coordinates, it can be used to explore other data types such as electron density maps, electrostatic potential maps, and sequence alignments, and it can be used to create high-quality images and movies for publication and presentation. For exploring broader biological contexts, RBVI also develops and distributes plugins to the open-source network visualization tool Cytoscape. Protein sequence or structure similarity networks, metabolic pathways, and networks of small molecule metabolites or drugs are a few examples of systems of interest. The plugins provide capabilities for manipulating and analyzing the networks and linking them to 3D visualization with Chimera. The Structure-Function Linkage Database (sfld.rbvi.ucsf.edu) connects evolutionarily related sequences and structures (superfamilies of enzymes) to their chemical reactions, and correlates conserved active site residues with specific partial reactions common to the members of a superfamily. It provides highly curated information on mechanistically diverse superfamilies, which catalyze many different overall reactions and have historically been subject to many annotation problems. This public resource can be used to guide functional annotation and protein engineering applications. The Sequence Analysis and Consulting Service (SACS, www.sacs.ucsf.edu) provides expertise in bioinformatics, molecular visualization and analysis, and network visualization and analysis. It also provides local access to up-to-date versions of sequence analysis software and sequence databases. As development continues, it is imperative that the RBVI team remains connected to the broader structural and molecular biology research and teaching community through outreach and training. These activities promote awareness of what the Resource has to offer, resulting in more effective use and driving further developments.

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 子项目的主要研究者可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 生物计算，可视化和信息学资源（RBVI）为基于计算和可视化的数据分析开发创新方法和算法，将其作为专业质量，易于使用的软件工具，并将这些工具应用于解决与分子序列，结构和功能有关的各种问题。 UCSF Chimera（www.cgl.ucsf.edu/chimera）是RBVI正在积极开发的分子建模软件包。嵌合体是一种用于可视化和分析生物分子结构和相互作用的工具。除了原子坐标之外，它还可以用于探索其他数据类型，如电子密度图，静电势图和序列比对，并且可以用于创建高质量的图像和电影以供出版和演示。 为了探索更广泛的生物背景，RBVI还开发和分发开源网络可视化工具Cytoscape的插件。 蛋白质序列或结构相似性网络、代谢途径和小分子代谢物或药物的网络是感兴趣的系统的一些示例。 这些插件提供了操纵和分析网络的功能，并将它们与Chimera的3D可视化连接起来。 结构-功能连锁数据库（sfld.rbvi.ucsf.edu）将进化相关的序列和结构（酶的超家族）与它们的化学反应联系起来，并将保守的活性位点残基与超家族成员常见的特定部分反应相关联。它提供了关于机械上不同的超家族的高度策划的信息，这些超家族催化许多不同的整体反应，并且在历史上受到许多注释问题的影响。该公共资源可用于指导功能注释和蛋白质工程应用。 序列分析和咨询服务（SACS，www.sacs.ucsf.edu）提供生物信息学，分子可视化和分析以及网络可视化和分析方面的专业知识。它还提供对最新版本的序列分析软件和序列数据库的本地访问。 随着发展的继续，RBVI团队必须通过推广和培训与更广泛的结构和分子生物学研究和教学社区保持联系。 这些活动提高了对资源所能提供的认识，从而更有效地利用资源并推动进一步的发展。