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Alex Moffett's Projects

alpha_helical_content icon alpha_helical_content

Python implementation of the NAMD alpha-helical content colvar (http://www.ks.uiuc.edu/Research/namd/2.9/ug/node55.html)

conshelix icon conshelix

Python implementation of helix CVs from Lee and Im, J. Comput. Chem. 2007

kl_divergence icon kl_divergence

Implementing the local Kullback-Leibler divergence measure from McClendon et al. JCTC 2012 in Python

langevin_dynamics icon langevin_dynamics

Langevin dynamics of a single particle in one and two dimensions in Python.

maxcal icon maxcal

Python implementation of MaxCal MSM reweighting from Wan, Zhou, and Voelz, JCTC (2016).

orgtraj icon orgtraj

Simplify storing metadata with featurized trajectories.

preferential_interaction_coefficient icon preferential_interaction_coefficient

Python scripts for calculating the preferential interaction coefficient and transfer free energy of proteins with cosolvents from molecular dynamics simulations.

tumor-immune_ecology_2023 icon tumor-immune_ecology_2023

Code for producing all results and figures from the manuscript "Modeling the role of immune cell conversion in the tumor-immune microenviroment".

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