Biomedical Technology Resources
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Resource for Biocomputing, Visualization, and Informatics

Thomas E. Ferrin, Ph.D.
P41-GM103311
Active

Center Overview

The Resource for Biocomputing, Visualization, and Informatics (RBVI) develops software and Web-based resources for the visualization and analysis of molecular structures and related data. Given the ever-expanding and increasingly heterogeneous universe of information on biological molecules - structural data at scales ranging from atomic to supramolecular, sequences, expression data, physical and genetic interactions, functional roles, associations with disease - researchers require truly integrative software to promote understanding of the data as a coherent whole. The RBVI creates tools for handling and integrating diverse types of biomolecular data, including atomic-resolution structures, density maps, sequence alignments, annotations, and networks, with an emphasis on interactive visualization. The center develops high-quality software that is downloaded thousands of times per month, provides training both directly and via online materials, and hosts several Web services and a unique enzyme structure-function database. Our close collaborations with other scientists ensure that RBVI developments directly address the challenges associated with applying computing and information technology to biomedicine, enable translational research, and facilitate building upon today's fundamental knowledge in structural and computational biology to elucidate cellular function.

Impact on Human Health

The RBVI aims to promote understanding of biomolecular sequence-structure-function relationships by providing professional-quality, thoroughly documented software and well-curated data to researchers and educators worldwide. Our extensive collaborations with researchers help to drive the development cycle; new tools allow exploring new avenues of research, leading to further questions and further developments.

More fundamentally, the software we develop and freely distribute is used to convey information, through images and animations, about molecular structures and analyses. Such information sharing is vital to the research enterprise, as breakthroughs generally come from the work of multiple laboratories. Visualization is also integral to teaching students at all levels about molecular structure and function, and engaging youth in science. These activities are essential to cultivating scientific literacy and the next generation of biomedical researchers.

Tags

Resources

ResourceDescriptionSupported PlatformsSupported FormatsData TypeData Size (compressed)
chemViz2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that links network visualization in Cytoscape with cheminformatics, namely 2D display of small molecules and calculation of chemical descriptors and Tanimoto similarities.

N/A N/A
Chimera (UCSF Chimera)
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A package for the interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, conformational ensembles, and trajectories.

Linux, Mac OSX, Windows Aligned FASTA, Aligned NBRF/PIR,...(more) N/A N/A
clusterMaker2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that provides several clustering methods and links between different displays of the results such as node hierarchies and heat maps.

N/A N/A
structureViz2
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A plugin to Cytoscape that links network visualization in Cytoscape with visualization and analysis of molecular structures in Chimera.

N/A N/A
Structure-Function Linkage Database
Resource for Biocomputing, Visualization, and Informatics
NIGMS

A highly curated database of enzyme families/superfamilies and associated sequence-structure-function relationships. Superfamilies are defined by a conserved chemical capability such as a partial reaction, families by a conserved overall reaction.

Database N/A