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.

该副本是利用资源的众多研究子项目之一 由NIH/NCRR资助的中心赠款提供。对该子弹的主要支持 而且，副投影的主要研究员可能是其他来源提供的 包括其他NIH来源。 列出的总费用可能 代表subproject使用的中心基础架构的估计量， NCRR赠款不直接向子弹或副本人员提供的直接资金。 生物计算，可视化和信息学的资源（RBVI）开发了用于基于计算和可视化数据分析的创新方法和算法，将其视为专业质量，易于使用的软件工具，并将工具应用于与分子序列，结构和功能有关的广泛问题。 UCSF Chimera（www.cgl.ucsf.edu/chimera）是RBVI在主动开发下的分子建模包。嵌合体是可视化和分析生物分子结构和相互作用的工具。除原子坐标外，还可以用于探索其他数据类型，例如电子密度图，静电势图和序列比对，可用于创建高质量的图像和电影以进行出版和演示。 为了探索更广泛的生物环境，RBVI还为开源网络可视化工具Cytoscape开发和分发插件。 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系统的一些例子。 该插件提供了操纵和分析网络并将其链接到3D可视化的功能。 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）连接到其化学反应，并将保守的活性位点残基与超级家庭成员共有的特定部分反应相关联。它提供了有关机械多样性超家族的高度策划信息，这些信息催化了许多不同的总体反应，并且从历史上却遇到了许多注释问题。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）提供了生物信息学，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。它还提供了对序列分析软件和序列数据库的最新版本的本地访问。 随着发展的继续，RBVI团队必须通过外展和培训与更广泛的结构和分子生物学研究和教学社区联系。 这些活动促进了人们对资源所提供的知识的认识，从而导致更有效的利用并推动进一步的发展。