Jupyter Notebooks for Molecular Dynamics
☆44Jul 13, 2025Updated last year
Alternatives and similar repositories for MDNotebooks
Users that are interested in MDNotebooks are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- fragbuilder is a tool to create, setup and analyze QM calculations on peptides.☆15Oct 31, 2014Updated 11 years ago
- ☆24Mar 21, 2024Updated 2 years ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆16Apr 3, 2026Updated 3 months ago
- Jupyter Dock is a set of Jupyter Notebooks for performing molecular docking protocols interactively, as well as visualizing, converting f…☆283Oct 30, 2023Updated 2 years ago
- How to start with Jupyter, Python, Libs, Github and Models☆13May 18, 2022Updated 4 years ago
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆20Updated this week
- A collection of scripts which I have developed to use GROMACS, for both compute clusters and post-simulation analysis.☆11Jul 15, 2014Updated 12 years ago
- ChEMBL Similarity Search☆19Nov 28, 2020Updated 5 years ago
- NAMD's psfgen + Python improvements☆16Sep 1, 2024Updated last year
- ☆10May 17, 2021Updated 5 years ago
- Cloud-based molecular simulations for everyone☆499Jan 20, 2026Updated 6 months ago
- Assessing the impact of mutations on antibody-antigen binding affinity☆18Dec 7, 2020Updated 5 years ago
- ☆10Feb 25, 2021Updated 5 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆35Jan 6, 2026Updated 6 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- ☆25Feb 28, 2023Updated 3 years ago
- Generate Ramachandran plots for single PDB structure and as heatmap for MD trajectory☆11Apr 6, 2022Updated 4 years ago
- a VMD plugin for binding affinity prediction using end-point free energy methods☆28Apr 23, 2016Updated 10 years ago
- Analysis of non-covalent interactions in MD trajectories☆69Jan 3, 2025Updated last year
- Python module for identification of conserved water molecules from molecular dynamics trajectories.☆15Updated this week
- Robust and stable clustering of molecular dynamics simulation trajectories.☆20Sep 2, 2022Updated 3 years ago
- Multi-Level DBSCAN: A Hierarchical Density-Based Clustering Method for Analyzing Molecular Dynamics Trajectories☆13Dec 6, 2020Updated 5 years ago
- Accelerated sampling framework with autoencoder-based method☆23Sep 7, 2019Updated 6 years ago
- Computational Chemistry☆27Jul 11, 2025Updated 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.
- binding free energy estimator 2☆146Jul 14, 2026Updated last week
- ☆126Feb 4, 2026Updated 5 months ago
- Program for robust fitting of bonded Molecular Mechanics parameters☆15Jun 30, 2015Updated 11 years ago
- Jupyter Notebooks for Python Introduction, University of Basel, May 2020☆14May 15, 2020Updated 6 years ago
- Making life easier using scripting languages (Bash and Python) to facilitate multiple VASP simulation jobs preparation, submission and an…☆13Dec 15, 2014Updated 11 years ago
- ☆11Apr 22, 2024Updated 2 years ago
- Introductory tutorial on TPS, committor analysis, and (MS)TIS with OpenPathSampling☆20Dec 15, 2025Updated 7 months ago
- ☆11Oct 18, 2019Updated 6 years ago
- ☆18Jul 26, 2024Updated last year
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- User Guide for MDAnalysis☆30Updated this week
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Mar 18, 2019Updated 7 years ago
- Spectral Gap Optimization of Parameters☆18Mar 28, 2020Updated 6 years ago
- Probabilistic Inference for NOvel Therapeutics☆15Feb 5, 2022Updated 4 years ago
- ☆14Sep 18, 2023Updated 2 years ago
- Resources for Learning Cheminformatics with the RDKit☆19Apr 7, 2019Updated 7 years ago
- A collection of cheminformatics utility functions for use with marimo notebooks☆20Jan 11, 2026Updated 6 months ago