The UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI) will continue its long history of developing software and advanced web-based resources for the integrated visualization and analysis of molecular structure at scales ranging from atomic to supramolecular. We will create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Our primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. We will provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. Through our Driving Biomedical Projects, we will enable scientists to understand, analyze, and illustrate to others the important principles of molecular recognition and interactions. All of the tools that we develop will be made available in binary and source code form via our web site. Researchers will be trained in the use of these tools and will be able to collaborate with RBVI staff. Dissemination of our technological developments and collaborative research results will be accomplished via scientific publications, lectures, software distribution, video animations, and though our web site: www.rbvi.ucsf.edu/.
The research tools we develop will directly address the challenges associated with applying computing and information technology to biomedicine, building out from today's fundemental knowledge in structural biology and computational biology, to provide insight into cellular function and tools for translational medicine.
|Schmid, G; Zeitvogel, F; Hao, L et al. (2014) 3-D analysis of bacterial cell-(iron)mineral aggregates formed during Fe(II) oxidation by the nitrate-reducing Acidovorax sp. strain BoFeN1 using complementary microscopy tomography approaches. Geobiology 12:340-61|
|Schmid, Gregor; Zeitvogel, Fabian; Hao, Likai et al. (2014) Synchrotron-based chemical nano-tomography of microbial cell-mineral aggregates in their natural, hydrated state. Microsc Microanal 20:531-6|
|Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E et al. (2014) The Structure-Function Linkage Database. Nucleic Acids Res 42:D521-30|
|Stroupe, M Elizabeth; Brewer, Tess E; Sousa, Duncan R et al. (2014) The structure of Sinorhizobium meliloti phage ?M12, which has a novel T=19l triangulation number and is the founder of a new group of T4-superfamily phages. Virology 450-451:205-12|
|Baler, K; Martin, O A; Carignano, M A et al. (2014) Electrostatic unfolding and interactions of albumin driven by pH changes: a molecular dynamics study. J Phys Chem B 118:921-30|
|Beard, William A; Shock, David D; Batra, Vinod K et al. (2014) Substrate-induced DNA polymerase ? activation. J Biol Chem 289:31411-22|
|Lunetta, Jennine M; Pappagianis, Demosthenes (2014) Identification, molecular characterization, and expression analysis of a DOMON-like type 9 carbohydrate-binding module domain-containing protein of Coccidioides posadasii. Med Mycol 52:591-609|
|Christie, Peter J; Whitaker, Neal; González-Rivera, Christian (2014) Mechanism and structure of the bacterial type IV secretion systems. Biochim Biophys Acta 1843:1578-91|
|Harvilla, Paul B; Wolcott, Holly N; Magyar, John S (2014) The structure of ferricytochrome c552 from the psychrophilic marine bacterium Colwellia psychrerythraea 34H. Metallomics 6:1126-30|
|Backus, Keriann M; Dolan, Michael A; Barry, Conor S et al. (2014) The three Mycobacterium tuberculosis antigen 85 isoforms have unique substrates and activities determined by non-active site regions. J Biol Chem 289:25041-53|
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