PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
☆337Feb 25, 2026Updated last week
Alternatives and similar repositories for propka
Users that are interested in propka are comparing it to the libraries listed below
Sorting:
- PDBFixer fixes problems in PDB files☆626Oct 30, 2025Updated 4 months ago
- Interaction Fingerprints for protein-ligand complexes and more☆477Feb 22, 2026Updated last week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆350Jan 6, 2026Updated 2 months ago
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆649Oct 30, 2025Updated 4 months ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆220Updated this week
- An open library for the analysis of molecular dynamics trajectories☆701Feb 27, 2026Updated last week
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆67Feb 1, 2024Updated 2 years ago
- Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm☆382Sep 16, 2025Updated 5 months ago
- pKa estimates for proteins using an ensemble approach☆29Jul 11, 2025Updated 7 months ago
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆442Sep 9, 2024Updated last year
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆166Feb 16, 2026Updated 2 weeks ago
- C-library for calculating Solvent Accessible Surface Areas☆179Nov 15, 2025Updated 3 months ago
- HTMD: Programming Environment for Molecular Discovery☆273Updated this week
- MoleculeKit: Your favorite molecule manipulation kit☆236Feb 25, 2026Updated last week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated 2 months ago
- Python interface of cpptraj☆188Jan 20, 2026Updated last month
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Jul 6, 2023Updated 2 years ago
- A Python Package for Protein Dynamics Analysis☆533Feb 13, 2026Updated 3 weeks ago
- the simple alchemistry library☆235Jan 23, 2026Updated last month
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 4 months ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆383Feb 25, 2026Updated last week
- An interoperable Python framework for biomolecular simulation.☆146Feb 25, 2026Updated last week
- The OpenMM Cookbook and Tutorials☆56Feb 11, 2026Updated 3 weeks ago
- Parameter/topology editor and molecular simulator☆448Jan 12, 2026Updated last month
- A deep learning framework for molecular docking☆865Feb 26, 2026Updated last week
- Analysis of non-covalent interactions in MD trajectories☆67Jan 3, 2025Updated last year
- Auto3D generates low-energy conformers from SMILES/SDF☆187Jan 22, 2026Updated last month
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆154Feb 27, 2026Updated last week
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆141Nov 10, 2025Updated 3 months ago
- A dependency-free cross-platform swiss army knife for PDB files.☆446Feb 3, 2026Updated last month
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Feb 9, 2026Updated 3 weeks ago
- Interface for AutoDock, molecule parameterization☆341Updated this week
- The Open Free Energy toolkit☆257Feb 27, 2026Updated last week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Feb 12, 2026Updated 3 weeks ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆168Jan 5, 2026Updated 2 months ago
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆298Dec 8, 2025Updated 2 months ago
- Open Drug Discovery Toolkit☆458Dec 13, 2022Updated 3 years ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆395Feb 26, 2026Updated last week
- End-To-End Molecular Dynamics (MD) Engine using PyTorch☆686Jan 7, 2026Updated 2 months ago