Software

The group has written and currently maintains several open-source software packages and online applications for scientific computing.

PigmentHunter is an open-source online app for structure-based spectroscopic calculations on chlorophyll-binding proteins. The app includes a graphical user interface accessed directly in a web browser (no download or install required), interactive structure viewing, automated molecular dynamics simulations, site-energy and inter-pigment coupling calculations, and excitonic methods for calculating the optical spectra of coupled pigments. The app is currently maintained by three group members: Mike Reppert, Safa Ahad, and Chientzu Lin.

AmideSpec is an open-source online app for structure-based Amide I spectroscopic calculations. The interface is similar to PigmentHunter but is currently used only for qualitative (educational) purposes. (The level of theory is too low for research-grade calculations.) Ultimately, AmideSpec will replace the g_amide and g_spec packages currently hosted on GitHub.

g_amide interfaces with the popular molecular dynamics package gromacs to predict Amide I vibrational frequencies for backbone carbonyl groups in peptides and proteins.

g_spec offers efficient numerical simulation of linear and 2D vibrational spectra. In conjunction with gromacs and g_amide, it offers a complete numerical library for converting protein structures into accurate Amide I vibrational spectra.