PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
☆363Mar 21, 2026Updated 3 months ago
Alternatives and similar repositories for propka
Users that are interested in propka 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☆661Mar 10, 2026Updated 3 months ago
- pKa estimates for proteins using an ensemble approach☆31Jun 26, 2026Updated last week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆374Jun 25, 2026Updated last week
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆68Mar 29, 2026Updated 3 months ago
- Interaction Fingerprints for protein-ligand complexes and more☆510Jun 21, 2026Updated 2 weeks ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆483Mar 9, 2026Updated 3 months ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆173Apr 26, 2026Updated 2 months ago
- An open library for the analysis of molecular dynamics trajectories☆724Jun 22, 2026Updated 2 weeks ago
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆696Updated this week
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆225Mar 4, 2026Updated 4 months ago
- Parameter/topology editor and molecular simulator☆452Updated this week
- Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm☆400Sep 16, 2025Updated 9 months ago
- MoleculeKit: Your favorite molecule manipulation kit☆237Jun 29, 2026Updated last week
- Experiments with expanded ensembles to explore chemical space☆202Oct 28, 2025Updated 8 months ago
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆331Jan 7, 2026Updated 5 months ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆179Mar 11, 2026Updated 3 months ago
- Python interface of cpptraj☆191Mar 6, 2026Updated 4 months ago
- HTMD: Programming Environment for Molecular Discovery☆274Updated this week
- C-library for calculating Solvent Accessible Surface Areas☆196May 31, 2026Updated last month
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆395Jun 30, 2026Updated last week
- the simple alchemistry library☆241Jun 1, 2026Updated last month
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆202Jul 6, 2023Updated 3 years ago
- The OpenMM Cookbook and Tutorials☆58Apr 28, 2026Updated 2 months ago
- AI Agents on DigitalOcean Gradient AI Platform • AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- A Python Package for Protein Dynamics Analysis☆554Updated this week
- Analysis of non-covalent interactions in MD trajectories☆69Jan 3, 2025Updated last year
- An interoperable Python framework for biomolecular simulation.☆165Jun 29, 2026Updated last week
- Auto3D generates low-energy conformers from SMILES/SDF☆193Jun 13, 2026Updated 3 weeks ago
- Automated Adaptive Absolute alchemical Free Energy calculator☆123May 1, 2026Updated 2 months ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆257May 20, 2026Updated last month
- The Open Free Energy toolkit☆302Updated this week
- A deep learning framework for molecular docking☆950Jun 29, 2026Updated last week
- A dependency-free cross-platform swiss army knife for PDB files.☆456Jun 10, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Dec 19, 2021Updated 4 years ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆143Nov 10, 2025Updated 7 months ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆169Jun 5, 2026Updated last month
- An open tool implementing some recommended practices for analyzing alchemical free energy calculations☆138May 24, 2024Updated 2 years ago
- A command line application to launch molecular dynamics simulations with OpenMM☆40Apr 7, 2022Updated 4 years ago
- Interface for AutoDock, molecule parameterization☆374Updated this week
- 📐 Symmetry-corrected RMSD in Python☆118Jun 22, 2026Updated 2 weeks ago