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 Retinal degeneration is a major genetic and age related cause of serious eye disease and blindness. Understanding the molecular interactions of natural and synthetic agonists and antagonists with the visual pigments can provide a new route to halting and possibly reversing such degeneration. This collaboration will utilize grid-enabled AutoLigand and AutoDock, as well as AutoDockTools to computationally, 1) characterize the ligand binding sites of the human rod and cone opsin proteins. 2) predict the binding modes and free energies of known agonists and inverse agonists and 3) explore new inverse agonists using AutoDock Tools interactive Autoligand enhanced interface to help design ligands with increased potency and specificity. The efficacy of the new inverse agonists will be validated using biochemical studies with the human opsin proteins to demonstrate protein ligand interactions.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
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Special Emphasis Panel (ZRG1-SBIB-C (40))
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University of California San Diego
Anatomy/Cell Biology
Schools of Medicine
La Jolla
United States
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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
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
Morgan, Ashley E; Pantoja, Joe Luis; Weinsaft, Jonathan et al. (2016) Finite Element Modeling of Mitral Valve Repair. J Biomech Eng 138:021009
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
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
Zhang, Qin; Cha, Deukhyun; Bajaj, Chandrajit (2015) Quality Partitioned Meshing of Multi-Material Objects. Procedia Eng 124:187-199
Bettadapura, Radhakrishna; Rasheed, Muhibur; Vollrath, Antje et al. (2015) PF2fit: Polar Fast Fourier Matched Alignment of Atomistic Structures with 3D Electron Microscopy Maps. PLoS Comput Biol 11:e1004289
Edwards, John; Daniel, Eric; Pascucci, Valerio et al. (2015) Approximating the Generalized Voronoi Diagram of Closely Spaced Objects. Comput Graph Forum 34:299-309
Rushdi, Ahmad A; Mitchell, Scott A; Bajaj, Chandrajit L et al. (2015) Robust All-quad Meshing of Domains with Connected Regions. Procedia Eng 124:96-108

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