Software Development

WEST

Sijia is a developer of WEST, which is a massively parallel software for large scale electronic structure calculations within many-body perturbation theory.

OpenMolcas

Sijia is a developer of the quantum chemistry software package OpenMolcas, which features multiconfigurational methods.

A webpage that summarizes the University of Minnesota contributions to OpenMolcas and the relevant citation information can be found here.

ActiveGEnSeMBLE

GEnSeMBLE is a software suite developed by multiple members from the Goddard Group at Caltech for computationally predicting the conformations of G protein-coupled receptors (GPCRs).

ActiveGEnSeMBLE is a strategy based partly on the usage of the GEnSeMBLE package. While GEnSeMBLE tends to bias towards the inactive-state conformations, ActiveGEnSeMBLE predicts ensembles of GPCR conformations along GPCR activation pathways, including the higher-energy active-state conformations relevant to the functions of GPCRs.

One key component of ActiveGEnSeMBLE is the identification of relevant states among the large number of possible GPCR conformations. The procedure has been detailed in Ref. 1, 2 below. Sijia authored a group of Python scripts (ActiveSearch) for this purpose, including ones used in conjuction with GEnSeMBLE and ones used for analyzing molecular dynamics trajectories, and they are available upon reasonable request.

Citations for ActiveGEnSeMBLE, including ActiveSearch:

  1. Sijia S. Dong, William A. Goddard III, Ravinder Abrol. Conformational and Thermodynamic Landscape of GPCR Activation From Theory and Computation. Biophys. J., 2016, 110 (12), 2618-2629. (Link)

  2. Sijia S. Dong, William A. Goddard III, Ravinder Abrol. Identifying Multiple Active Conformations in the G Protein-Coupled Receptor Activation Landscape Using Computational Methods. Methods in Cell Biology, 2017, 142, 173-186. (Link)

Others

This webpage only contains information of software or scripts available to the public. For others, please contact us or co-authors of the associated publications for details.