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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App.
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Acknowledgements
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Outline
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PigmentHunter Interface and Workflow Applications and Examples
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Motivation
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Checklist:
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PigmentHunter: The 'Point-and-Click' Simulation Tool
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Background and Significance
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An Overview of PigmentHunter's Workflow
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Background and Significance
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Main Window 1. Characterizing Pigments
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nanoHub Embedded Libraries
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iPywidgets 1. Characterizing Pigments
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NGLView 1. Characterizing Pigments
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Pigments
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Outline
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Pigment Repairs and Biosymmetry Operations
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Pigment Repairs and Biosymmetry Operations
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Protein Repairs and Mutations
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Protein Repairs and Mutations
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Background and Significance
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Molecular Dynamics MD Organizer
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PyMol and Gromacs Implementation
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Outline
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Structure-Spectrum Connection
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The Frenkel Exciton Model
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Exciton Menu and Spectrum Calculation Window
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Exciton Menu and Spectrum Calculation Window
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Brief Overview and File Organization
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Outline
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Predicting Experimental Electrostatic Frequency Shifts
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Predicting Experimental Electrostatic Frequency Shifts
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Ring Distortion Site Energies with PSI and PSII
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Ring Distortion Site Energies with PSI and PSII
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Site Energy Calculations for Low Symmetry FMO Complex
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Site Energy Calculations for Low Symmetry FMO Complex
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Site Energy Calculations for Low Symmetry FMO Complex
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Site Energy Calculations for Low Symmetry FMO Complex
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Site Energy Calculations for Low Symmetry FMO Complex
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Adjusting Excitonic Parameters with LH2
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Conclusions
Description:
Explore the development and functionality of PigmentHunter, a nanoHUB online tool for simulating excitonic spectra of chlorophyll proteins using molecular dynamics. Learn how this graphical interface streamlines the process of running and analyzing protein simulations through a user-friendly "point-and-click" system. Discover the tool's workflow, including pigment characterization, protein repairs, molecular dynamics organization, and spectrum calculations based on the Frenkel Exciton Model. Gain insights into the implementation of current excitonic theories and the tool's applications in computational and experimental research. Understand how PigmentHunter leverages nanoHUB's science gateway to connect a graphical interface with high-performance computing capabilities, demonstrating the platform's potential for scientific application development.

Building a Graphical Interface for Exploring Protein Dynamics and Spectroscopy - PigmentHunter

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Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App.