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1037. An external point-charge model for wavelength regulation in visual pigments
1236. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement
96. a-ARM: Automatic Rhodopsin Modeling with Chromophore Cavity Generation, Ionization State Selection, and External Counterion Placement
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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
Using an Automated External Defibrillator (AED)