delemottelab

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10 repositories

KcsA_string_method_FES
Public
Code to generate the data and figures of the ion channel KcsA string method simulation project.
Jupyter Notebook
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MIT License
•1•1•0•0•Updated Apr 9, 2023Apr 9, 2023
string-method-swarms-trajectories
Public
A python implementation of the string method with swarms of trajectories using GROMACS
Python
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MIT License
•5•17•10•0•Updated Oct 19, 2022Oct 19, 2022
electroporation_MD-CG_machine_learning
Public
In this project we study electroporation of membranes with realistic compositions using coarse-grained molecular dynamics simulations combined with machine learning and bayesian statistics.
0•0•0•0•Updated Aug 23, 2022Aug 23, 2022
InfleCS-free-energy-clustering-tutorial
Public
Python tutorial for estimating and clustering free energy landscapes with InfleCS.
molecular-dynamics free-energy inflecs clustering
Jupyter Notebook
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MIT License
•16•26•0•0•Updated May 6, 2022May 6, 2022
allosteric-pathways
Public
Building and analyzing residue interaction networks with cofactors (includes tutorial).
molecular-dynamics network-analysis molecular-dynamics-analysis currrent-flow
Python
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MIT License
•8•17•1•0•Updated Mar 31, 2021Mar 31, 2021
gpcr-string-method-2019
Public
molecular-dynamics enhanced-sampling string-method free-energy-calculations gpcr
Python
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MIT License
•3•1•0•0•Updated Feb 2, 2021Feb 2, 2021
Informing_NMR_experiments_w_MD
Public
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
Jupyter Notebook
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MIT License
•1•0•0•0•Updated Dec 18, 2020Dec 18, 2020
demystifying
Public
machine-learning molecular-dynamics deep-taylor-decomposition biomolecular-simulation
Python
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MIT License
•8•19•9•0•Updated Jun 26, 2020Jun 26, 2020
state-sampling
Public
Python code for finding single equlibirated states and analysis of GPCR data
Python
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MIT License
•1•0•0•0•Updated Jun 23, 2020Jun 23, 2020
GMM-free-energy-estimator_code-used-in-paper
Public
MATLAB
•1•1•0•0•Updated Nov 29, 2017Nov 29, 2017