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

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 nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App.
Acknowledgements
Outline
PigmentHunter Interface and Workflow Applications and Examples
Motivation
Checklist:
PigmentHunter: The 'Point-and-Click' Simulation Tool
Background and Significance
An Overview of PigmentHunter's Workflow
Background and Significance
Main Window 1. Characterizing Pigments
nanoHub Embedded Libraries
iPywidgets 1. Characterizing Pigments
NGLView 1. Characterizing Pigments
Pigments
Outline
Pigment Repairs and Biosymmetry Operations
Pigment Repairs and Biosymmetry Operations
Protein Repairs and Mutations
Protein Repairs and Mutations
Background and Significance
Molecular Dynamics MD Organizer
PyMol and Gromacs Implementation
Outline
Structure-Spectrum Connection
The Frenkel Exciton Model
Exciton Menu and Spectrum Calculation Window
Exciton Menu and Spectrum Calculation Window
Brief Overview and File Organization
Outline
Predicting Experimental Electrostatic Frequency Shifts
Predicting Experimental Electrostatic Frequency Shifts
Ring Distortion Site Energies with PSI and PSII
Ring Distortion Site Energies with PSI and PSII
Site Energy Calculations for Low Symmetry FMO Complex
Site Energy Calculations for Low Symmetry FMO Complex
Site Energy Calculations for Low Symmetry FMO Complex
Site Energy Calculations for Low Symmetry FMO Complex
Site Energy Calculations for Low Symmetry FMO Complex
Adjusting Excitonic Parameters with LH2
Conclusions