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/.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Biotechnology Resource Grants (P41)
Project #
5P41GM103311-37
Application #
8667483
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Friedman, Fred K
Project Start
1997-07-15
Project End
2017-05-31
Budget Start
2014-06-01
Budget End
2015-05-31
Support Year
37
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Vallbracht, Melina; Rehwaldt, Sascha; Klupp, Barbara G et al. (2018) Functional Role of N-Linked Glycosylation in Pseudorabies Virus Glycoprotein gH. J Virol 92:
Adeyemo, Adebowale; Esezobor, Christopher; Solarin, Adaobi et al. (2018) HLA-DQA1 and APOL1 as Risk Loci for Childhood-Onset Steroid-Sensitive and Steroid-Resistant Nephrotic Syndrome. Am J Kidney Dis 71:399-406
Souza, Clarice de Azevedo; Richards, Kristian L; Park, YoSon et al. (2018) The YscE/YscG chaperone and YscF N-terminal sequences target YscF to the Yersinia pestis type III secretion apparatus. Microbiology 164:338-348
Bohl, Thomas E; Ieong, Pek; Lee, John K et al. (2018) The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release. J Biol Chem 293:7969-7981
Gao, Yong; McKay, Paul F; Mann, Jamie F S (2018) Advances in HIV-1 Vaccine Development. Viruses 10:
Orbán-Németh, Zsuzsanna; Beveridge, Rebecca; Hollenstein, David M et al. (2018) Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data. Nat Protoc 13:478-494
Maruyama, Yutaka; Mitsutake, Ayori (2018) Analysis of Structural Stability of Chignolin. J Phys Chem B 122:3801-3814
Kontur, Wayne S; Bingman, Craig A; Olmsted, Charles N et al. (2018) Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the ?-aryl ether bond of lignin. J Biol Chem 293:4955-4968
Tokmina-Roszyk, Michal; Fields, Gregg B (2018) Dissecting MMP P10' and P11' subsite sequence preferences, utilizing a positional scanning, combinatorial triple-helical peptide library. J Biol Chem 293:16661-16676
Rosenberg, Masha M; Redfield, Alfred G; Roberts, Mary F et al. (2018) Dynamic Characteristics of Guanosine-5'-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry. Biochemistry 57:3146-3154

Showing the most recent 10 out of 272 publications