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. (A) OBJECTIVES The RCSB Protein Data Bank (PDB) is an international repository for three-dimensional macromolecular structure data (Berman et al., 2000). The RCSB team, directed by Prof. Helen Berman, is in the process of applying for a new five-year grant to operate the PDB. This collaborative project will synergize activities proposed in each respective projects renewal. As a result both projects will be stronger and more valuable to a community of users than would otherwise be the case. This synergistic effort has the following goals for each resource: For PDB: + NBCR will provide a vehicle to distribute and use protein functional site search information generated by the PDB and provided as a Web service. The method of site search is yet to be determined and will be evaluated by the PDB in the early stages of the renewal. The intent is to provide details of similar binding sites that have implications for a variety of studies from evolutionary relationships to drug discovery. + NBCR will provide a distributed environment to support the computation of data associated with 3-dimensional structure comparison. The PDB renewal calls for these data initially being calculated by the FatCat method (Ye and Godzik 2004) that provides for protein flexibility. Later other methods will be evaluated. In either case computation of an all-by-all protein structure comparison is a high performance task that can benefit from the NBCR infrastructure. For NBCR: PDB will provide high visibility and audience for services that include: + Passing the results of structure comparisons and other data to applications through NBCR middleware. + Provision of a testbed for grid services. + Provision by NBCR of electrostatic data to be included as part of PDB services (this provision was not in the PDB renewal application but is deemed a useful addition).

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR008605-18
Application #
8362805
Study Section
Special Emphasis Panel (ZRG1-SBIB-C (40))
Project Start
2011-05-01
Project End
2012-04-30
Budget Start
2011-05-01
Budget End
2012-04-30
Support Year
18
Fiscal Year
2011
Total Cost
$39,987
Indirect Cost
Name
University of California San Diego
Department
Anatomy/Cell Biology
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Pantoja, Joe Luis; Morgan, Ashley E; Grossi, Eugene A et al. (2017) Undersized Mitral Annuloplasty Increases Strain in the Proximal Lateral Left Ventricular Wall. Ann Thorac Surg 103:820-827
Morgan, Ashley E; Wozniak, Curtis J; Gulati, Sarthak et al. (2017) Association of Uneven MitraClip Application and Leaflet Stress in a Finite Element Model. JAMA Surg 152:111-114
Ebeida, Mohamed S; Rushdi, Ahmad A; Awad, Muhammad A et al. (2016) Disk Density Tuning of a Maximal Random Packing. Comput Graph Forum 35:259-269
Bucero, Marta Abril; Bajaj, Chandrajit; Mourrain, Bernard (2016) On the construction of general cubature formula by flat extensions. Linear Algebra Appl 502:104-125
Ge, Liang; Wu, Yife; Soleimani, Mehrdad et al. (2016) Moderate Ischemic Mitral Regurgitation After Posterolateral Myocardial Infarction in Sheep Alters Left Ventricular Shear but Not Normal Strain in the Infarct and Infarct Borderzone. Ann Thorac Surg 101:1691-9
Watson, Shana R; Liu, Piaomu; Peña, Edsel A et al. (2016) Comparison of Aortic Collagen Fiber Angle Distribution in Mouse Models of Atherosclerosis Using Second-Harmonic Generation (SHG) Microscopy. Microsc Microanal 22:55-62
Morgan, Ashley E; Pantoja, Joe L; Grossi, Eugene A et al. (2016) Neochord placement versus triangular resection in mitral valve repair: A finite element model. J Surg Res 206:98-105
Purvine, Emilie; Monson, Kyle; Jurrus, Elizabeth et al. (2016) Energy Minimization of Discrete Protein Titration State Models Using Graph Theory. J Phys Chem B 120:8354-60
Morgan, Ashley E; Pantoja, Joe Luis; Weinsaft, Jonathan et al. (2016) Finite Element Modeling of Mitral Valve Repair. J Biomech Eng 138:021009
Zhang, Qin; Cha, Deukhyun; Bajaj, Chandrajit (2015) Quality Partitioned Meshing of Multi-Material Objects. Procedia Eng 124:187-199

Showing the most recent 10 out of 269 publications