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 structures. PigmentHunter utilizes and illustrates the extent of nanoHUB’s capabilities with application development. Built using a Jupyter Notebook environment, PigmentHunter uses the nanoHUB science gateway to link a graphical user interface to a high-performance computing backend. This tool classifies recognized pigments in the protein complexes and runs gas-phase molecular dynamics to build excitonic models and predict their optical spectra. We will discuss how current excitonic theories were implemented into this novel interface as well as its different computational and experimental applications.

Safa Ahad completed her chemistry B.S. at West Virginia University in 2019. She is now a physical chemistry PhD candidate at Purdue University. Her research is a mixture of computation and experiment, focusing on the optical spectra shifts in photosynthetic protein complexes. Safa is currently working on a collaborative project between the Reppert and Slipchenko groups focusing on the development and automation of quantum mechanics/molecular mechanics models and new coupling models for tightly spaced chlorophyll dimers. She is planning for a career in computational modeling and simulation for protein-ligand systems.

Network for Computational Nanotechnology

Researchers should cite this work as follows:

• Safa Ahad (2024), "Building a nanoHUB Graphical Interface for Exploring Protein Dynamics and Spectroscopy: the PigmentHunter App," https://nanohub.org/resources/38899.

  BibTex | EndNote

1. chemistry
2. computational chemistry
3. materials science
4. molecular dynamics (MD)
5. molecular spectroscopy
6. optical properties
7. photosynthetic proteins
8. PigmentHunter
9. pigments
10. proteins