delemottelab

InfleCS-free-energy-clustering-tutorial

Python tutorial for estimating and clustering free energy landscapes with InfleCS.

demystifying

string-method-swarms-trajectories

A python implementation of the string method with swarms of trajectories using GROMACS

allosteric-pathways

Building and analyzing residue interaction networks with cofactors (includes tutorial).

GMM-free-energy-estimator_code-used-in-paper

gpcr-string-method-2019

KcsA_string_method_FES

Code to generate the data and figures of the ion channel KcsA string method simulation project.

electroporation_MD-CG_machine_learning

In this project we study electroporation of membranes with realistic compositions using coarse-grained molecular dynamics simulations combined with machine learning and bayesian statistics.

Informing_NMR_experiments_w_MD

Code for: Informing NMR experiments with molecular dynamics simulations to characterize the dominant open state of KcsA. https://doi.org/10.1101/2020.12.14.422800

state-sampling

Python code for finding single equlibirated states and analysis of GPCR data