Biomolecular Dynamics

Group of Prof. Dr. G. Stock, University of Freiburg

Welcome at MolDyn Freiburg 👋

Understanding elementary life processes from first principles.

Working in theoretical biological physics in close collaboration with experimental groups, we areconcerned with the theory and simulation of elementary biomolecular processes. In particular, westrive to design new multiscale simulation methods and develop novel strategies to reduce thecomplexity of nonequilibrium phenomena.

Checkout our website for a list of allpublications 📚,fields of research :atom: 🧬🔬, or to get incontactwith us.

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MoSAICMoSAICPublic
Correlation-based feature selection of Molecular Dynamics simulations
Python 27 2
ClusteringClusteringPublic
Robust and stable clustering of molecular dynamics simulation trajectories.
C++ 18 6
dcTMDdcTMDPublic
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
Python 14
msmhelpermsmhelperPublic
Helper function for Markov State Models
Python 9 3
FastPCAFastPCAPublic
Forked fromlettis/FastPCA
Fast, parallelized implementation of Principal Component Analysis with constant memory consumption for large data sets.
C 9 2
MSMPathfinderMSMPathfinderPublic
Finding pathways from an Markov State Model
C++ 9 3

Repositories

Showing 10 of 21 repositories

NorMI Public
Generalized Kraskov Estimator for Normalized Mutual Information
moldyn/NorMI’s past year of commit activity
Python 14MIT 1 3 0 UpdatedNov 21, 2024
MoSAIC Public
Correlation-based feature selection of Molecular Dynamics simulations
moldyn/MoSAIC’s past year of commit activity
Python 27MIT 2 2 1 UpdatedNov 19, 2024
dcTMD Public
Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.
moldyn/dcTMD’s past year of commit activity
Python 14MIT0 1 2 UpdatedJul 17, 2024
tutorial_dcTMD Public Forked fromfloWneffetS/tutorial_dcTMD
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
moldyn/tutorial_dcTMD’s past year of commit activity
Python 2GPL-3.0 4 0 0 UpdatedJul 15, 2024
msmhelper Public
Helper function for Markov State Models
moldyn/msmhelper’s past year of commit activity
Python 9BSD-3-Clause 3 0 1 UpdatedJun 25, 2024
HP35 Public
Selecting Features for Markov Modeling: A Case Study on HP35
moldyn/HP35’s past year of commit activity
HiveQL 8BSD-3-Clause 1 1 0 UpdatedMay 25, 2023
HP35-DESRES Public
DESRES trajectory of wild type HP-35 at 360K
moldyn/HP35-DESRES’s past year of commit activity
50 0 0 UpdatedMay 16, 2023
2Dmodel_path_analysis Public Forked fromfloWneffetS/2Dmodel_path_analysis
Jupyter notebook with 2D test potential energy landscape for performing model biased simulations combined with pathway analysis.
moldyn/2Dmodel_path_analysis’s past year of commit activity
Jupyter Notebook 1 1 0 0 UpdatedJan 16, 2023
Clustering Public
Robust and stable clustering of molecular dynamics simulation trajectories.
moldyn/Clustering’s past year of commit activity
C++ 18BSD-2-Clause 6 1 0 UpdatedSep 2, 2022
HP35-Benchmark Public
Benchmarking dimensionality reduction methods and clustering on HP35-DESRES
moldyn/HP35-Benchmark’s past year of commit activity
Shell 1BSD-3-Clause0 0 0 UpdatedAug 5, 2022