A Python Package for Protein Dynamics Analysis
☆536Mar 9, 2026Updated last month
Alternatives and similar repositories for ProDy
Users that are interested in ProDy are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- PDBFixer fixes problems in PDB files☆637Mar 10, 2026Updated 3 weeks ago
- Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm☆388Sep 16, 2025Updated 6 months ago
- An open library for the analysis of molecular dynamics trajectories☆707Mar 31, 2026Updated last week
- Interaction Fingerprints for protein-ligand complexes and more☆488Mar 30, 2026Updated last week
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆345Mar 21, 2026Updated 2 weeks ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆664Oct 30, 2025Updated 5 months ago
- MoleculeKit: Your favorite molecule manipulation kit☆236Apr 2, 2026Updated last week
- A dependency-free cross-platform swiss army knife for PDB files.☆450Feb 3, 2026Updated 2 months ago
- A Python API for the RCSB Protein Data Bank (PDB)☆334Mar 30, 2026Updated last week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆354Apr 1, 2026Updated last week
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆410Apr 3, 2026Updated last week
- A comprehensive library for computational molecular biology☆936Apr 3, 2026Updated last week
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆218Jul 29, 2024Updated last year
- C-library for calculating Solvent Accessible Surface Areas☆182Nov 15, 2025Updated 4 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- Working with molecular structures in pandas DataFrames☆752Aug 1, 2024Updated last year
- A deep learning framework for molecular docking☆886Feb 26, 2026Updated last month
- Python interface of cpptraj☆190Mar 6, 2026Updated last month
- An interoperable Python framework for biomolecular simulation.☆152Mar 26, 2026Updated 2 weeks ago
- Parameter/topology editor and molecular simulator☆452Updated this week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆319Jan 7, 2026Updated 3 months ago
- HTMD: Programming Environment for Molecular Discovery☆274Mar 27, 2026Updated 2 weeks ago
- A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2☆98Aug 29, 2023Updated 2 years ago
- Jupyter widget to interactively view molecular structures and trajectories☆918Feb 2, 2026Updated 2 months ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- An all-atom protein structure dataset for machine learning.☆363Mar 16, 2024Updated 2 years ago
- OpenMM is a toolkit for molecular simulation using high performance GPU code.☆1,835Updated this week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆167Feb 16, 2026Updated last month
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆457Mar 9, 2026Updated last month
- WESTPA: The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis☆213Apr 2, 2026Updated last week
- Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196☆268Feb 10, 2026Updated last month
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆149Feb 12, 2025Updated last year
- TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data☆981Apr 1, 2026Updated last week
- Joint sequence and structure generation with RoseTTAFold sequence space diffusion☆331Oct 28, 2024Updated last year
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting with the flexibility to host WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Cloudways by DigitalOcean.
- EquiBind: geometric deep learning for fast predictions of the 3D structure in which a small molecule binds to a protein☆541Feb 19, 2025Updated last year
- End-To-End Molecular Dynamics (MD) Engine using PyTorch☆695Jan 7, 2026Updated 3 months ago
- OmegaFold Release Code☆617Dec 12, 2022Updated 3 years ago
- A simplified implementation of DSSP algorithm for PyTorch and NumPy☆100Jun 9, 2025Updated 10 months ago
- Cloud-based molecular simulations for everyone☆478Jan 20, 2026Updated 2 months ago
- Diffusion-based all-atom protein generative model.☆233Aug 27, 2025Updated 7 months ago
- AlphaFold Meets Flow Matching for Generating Protein Ensembles☆520Mar 22, 2026Updated 2 weeks ago