Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.
☆26Aug 15, 2024Updated last year
Alternatives and similar repositories for GME_tutorials
Users that are interested in GME_tutorials are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- TS-DAR identifies transition states of protein conformational changes from MD simulations using hyperspherical embeddings in the latent s…☆21May 15, 2026Updated last week
- A step-by-step tutorial to run Molecular Dynamics Simulations with enhanced sampling of a pepitide using PLUMED implemented in GROMACS to…☆16Mar 4, 2024Updated 2 years ago
- [ICML 2025] Repurposing pre-trained score-based generative models for transition path sampling by minimizing the Onsager-Machlup (OM) act…☆27Mar 20, 2026Updated 2 months ago
- A fast sampling and analysis tool for biomolecules☆17May 2, 2026Updated 3 weeks ago
- mdml: Deep Learning for Molecular Simulations☆55May 17, 2025Updated last year
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Repository of the data for PLUMED Masterclass 22.3☆14Jul 10, 2024Updated last year
- Main code repository for the PLUMED-GUI plugin for VMD☆17Jan 22, 2026Updated 4 months ago
- Using neural networks for enhanced sampling in computational biophysics☆16Aug 17, 2017Updated 8 years ago
- ☆13Jun 11, 2024Updated last year
- Python package for site-directed spin labeling of proteins☆14Updated this week
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Jan 26, 2022Updated 4 years ago
- Helper function for Markov State Models☆11Jun 25, 2024Updated last year
- Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.☆11Jul 15, 2024Updated last year
- Modeling with limited data☆63Dec 15, 2025Updated 5 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- Generative backmapping of coarse-grained molecular systems using an equivariant graph neural network and flow-matching☆12Sep 17, 2025Updated 8 months ago
- Scatterbar - data visualization for proportional data across many spatially resolved coordinates☆11Mar 3, 2025Updated last year
- Reweighted Autoencoded Variational Bayes for Enhanced Sampling (RAVE)☆44May 3, 2020Updated 6 years ago
- USC's Introduction to Health Data Science☆17Nov 26, 2025Updated 5 months ago
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆18Jun 30, 2025Updated 10 months ago
- Statistical models for biomolecular dynamics☆44May 8, 2025Updated last year
- ☆14May 13, 2020Updated 6 years ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆62Apr 6, 2026Updated last month
- Markov State Models on the Muller potential: a MSMBuilder Tutorial☆12Mar 18, 2013Updated 13 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- Weighted Ensemble simulation framework in Python☆61May 6, 2026Updated 2 weeks ago
- ☆20Jun 26, 2020Updated 5 years ago
- Prediction by Partial Matching☆16Apr 3, 2020Updated 6 years ago
- This repository provides with custom code and analysis scripts to generate structural ensembles of intrinsically disordered proteins by u…☆23Oct 31, 2025Updated 6 months ago
- Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories☆13Dec 6, 2020Updated 5 years ago
- Comparison of principal components analysis with diffusion maps on toy data sets and a molecular simulation trajectory☆17Feb 1, 2017Updated 9 years ago
- Python package for data analysis for dipolar EPR spectroscopy☆22Apr 17, 2026Updated last month
- Benchmarking code accompanying the release of `bioemu`☆61Apr 24, 2026Updated last month
- Parallel Molecular Docking using PLANTS software☆14Dec 8, 2024Updated last year
- Deploy on Railway without the complexity - Free Credits Offer • AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- How to analyze molecular dynamics data with PyEMMA☆86May 29, 2019Updated 6 years ago
- Predict allosteric pockets on proteins☆15Mar 28, 2022Updated 4 years ago
- PCA and normal mode analysis of proteins☆21May 16, 2024Updated 2 years ago
- Generative modeling of molecular dynamics trajectories☆216Mar 22, 2026Updated 2 months ago
- code for SeqDance/ESMDance, biophysics-informed protein language models☆59Jan 28, 2026Updated 3 months ago
- Instructions for Building Software on Various Platforms☆17May 12, 2025Updated last year
- Quantum to Molecular Mechanics (Q2MM)☆25May 8, 2026Updated 2 weeks ago