Description

 

PigmentHunter is a simulation tool searches protein data bank (PDB) files for photosynthetic pigments (currently chlorophyll a, chlorophyll b, pheophytin a, bacteriochlorophyll a are supported), and uses a vacuum-phase transition electrostatic potential (TrESP) model to calculate inter-site electronic couplings and the Qy absorption spectrum for the protein. The Charge Density Coupling (CDC) [Photosynth Res 95, 197 (2008)] and normal-coordinate structural decomposition (NSD) models can also be used to predict pigment site energies based on local electrostatics and/or ring deformation. 

Run Tool

All Categories (1-2 of 2)

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

   Online Presentations | 18 Apr 2024 | Contributor(s):: Safa Ahad

   Running and analyzing protein molecular dynamics (MD) simulations can be time consuming and tedious. In this webinar, we introduce PigmentHunter , an online nanoHUB tool that enables “point-and-click” MD-based simulation of excitonic spectra of chlorophyll proteins based on PDB...

2. Photosynthetic Protein Spectroscopy Lab

   Tools | 19 Oct 2020 | Contributor(s):: Safa Ahad, Chientzu Lin, Michael Earl Reppert

   This tool parses PDB structures of photosynthetic proteins to identify pigments, calculate inter-pigment interactions, and simulate optical spectra for the complex.