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105. highroad is induced by retinoids and clears mutant Rhodopsin-1 in Drosophila Retinitis Pigmentosa models
109. On the accuracy of retinal protonated Schiff base models
12 On the accuracy of retinal protonated Schiff base models
1288. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation
1380. Recent insights into the mechanisms underlying light-dependent retinal degeneration from X. laevis models of retinitis pigmentosa
1437. Photochemistry of visual pigment chromophore models by ab initio molecular dynamics
1507. Photoisomerization acceleration in retinal protonated Schiff-base models
152 Probing the rhodopsin cavity with reduced retinal models at the CASPT2//CASSCF/AMBER level of theory
1784. Models of ionic transport in biological membranes. Raman spectroscopy as a probe of valinomycin, gramicidin A', and rhodopsin conformations
1955 Bel Air
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20 Geometry optimization in polarizable QM/MM models: The induced dipole formulation
20 Modelling retinal chromophores photoisomerization: from minimal models in vacuo to ultimate bidimensional spectroscopy in rhodopsins
214. Geometry Optimization in Polarizable QM/MM Models: The Induced Dipole Formulation
25. Models in 3D Space (1869-1877); Optical Isomers
315. Recent insights into the mechanisms underlying light-dependent retinal degeneration from X. laevis models of retinitis pigmentosa
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41 Ab initio molecular dynamics of visual pigment chromophore models
436. Photochemistry of Visual Pigment Chromophore Models by Ab Initio Molecular Dynamics
530. Ab Initio Modeling of the Spatial, Electronic, and Vibrational Structure of Schiff Base Models for Visual Photoreceptors
55 Photoisomerization acceleration in retinal protonated Schiff-base models
576. Probing the Rhodopsin Cavity with Reduced Retinal Models at the CASPT2//CASSCF/AMBER Level of Theory
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828. Synthesis of retinals with eight- and nine-membered rings in the side chain. Models for rhodopsin photobleaching intermediates
84 Ab initio study of the carbon-13 NMR chemical shifts for some polyene compounds as models for the chromophore of rhodopsin.
98. Assessment of MC-PDFT Excitation Energies for a Set of QM/MM Models of Rhodopsins
A Comparison Between Bohr, Rutherford, and Quantum Mechanical Models
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Advances in experimental medicine and biology (2010), 664509-15, 1380. Recent insights into the mechanisms underlying light-dependent retinal degeneration from X. laevis models of retinitis pigmentosa
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The Automatic Rhodopsin Modeling (ARM) protocol, has recently been proposed as a tool for the fast and parallel generation of basic hybrid quantum mechanics/mol. mechanics (QM/MM) models of wild-type and mutant rhodopsins. However, in its present version, the input prepn. requires a few hour long user's manipulation of the template protein structure which also impairs the reproducibility of the generated models. This limitation, which makes the model building semi-automatic rather than fully automatic, comprises four tasks: the definition of the retinal chromophore cavity, the assignment of the protonation states of the ionizable residues, the neutralization of the protein with external counter-ions and, finally, the congruous generation of single or multiple mutations. In this work, the authors show that the automation of the original ARM protocol can be extended to a level suitable for performing the above tasks without user's manipulation and with an input prepn. time of minutes. The new protocol, call
The journal of physical chemistry. B (2007), 111(14), 3782-8, 1437. Photochemistry of visual pigment chromophore models by ab initio molecular dynamics
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