jensengroup / propkaView external linksLinks
PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.
☆334Jan 25, 2026Updated 3 weeks ago
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☆622Oct 30, 2025Updated 3 months ago
- Interaction Fingerprints for protein-ligand complexes and more☆474Feb 1, 2026Updated last week
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆348Jan 6, 2026Updated last month
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆644Oct 30, 2025Updated 3 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…☆219Jan 27, 2026Updated 2 weeks ago
- An open library for the analysis of molecular dynamics trajectories☆697Feb 4, 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☆379Sep 16, 2025Updated 4 months ago
- pKa estimates for proteins using an ensemble approach☆29Jul 11, 2025Updated 7 months ago
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆166Dec 7, 2025Updated 2 months ago
- fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scien…☆440Sep 9, 2024Updated last year
- C-library for calculating Solvent Accessible Surface Areas☆176Nov 15, 2025Updated 3 months ago
- HTMD: Programming Environment for Molecular Discovery☆272Nov 27, 2025Updated 2 months ago
- MoleculeKit: Your favorite molecule manipulation kit☆235Feb 5, 2026Updated last week
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated last month
- An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.☆193Jul 6, 2023Updated 2 years ago
- Python interface of cpptraj☆188Jan 20, 2026Updated 3 weeks ago
- A Python Package for Protein Dynamics Analysis☆526Updated this week
- the simple alchemistry library☆232Jan 23, 2026Updated 3 weeks ago
- Experiments with expanded ensembles to explore chemical space☆199Oct 28, 2025Updated 3 months ago
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆381Jan 22, 2026Updated 3 weeks ago
- An interoperable Python framework for biomolecular simulation.☆145Updated this week
- The OpenMM Cookbook and Tutorials☆54Updated this week
- Parameter/topology editor and molecular simulator☆448Jan 12, 2026Updated last month
- A deep learning framework for molecular docking☆855Dec 23, 2025Updated last month
- Analysis of non-covalent interactions in MD trajectories☆66Jan 3, 2025Updated last year
- Auto3D generates low-energy conformers from SMILES/SDF☆187Jan 22, 2026Updated 3 weeks ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆152Jan 22, 2026Updated 3 weeks ago
- An Open-Source Molecular Builder and Free Energy Preparation Workflow☆139Nov 10, 2025Updated 3 months ago
- A dependency-free cross-platform swiss army knife for PDB files.☆443Feb 3, 2026Updated last week
- Automated Adaptive Absolute alchemical Free Energy calculator☆114Jan 26, 2026Updated 2 weeks ago
- The Open Free Energy toolkit☆249Updated this week
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Jan 26, 2026Updated 2 weeks ago
- Interface for AutoDock, molecule parameterization☆335Feb 2, 2026Updated last week
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆295Dec 8, 2025Updated 2 months ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆167Jan 5, 2026Updated last month
- Open Drug Discovery Toolkit☆459Dec 13, 2022Updated 3 years ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆390Updated this week
- Quantum Mechanical Bespoke Force Field Derivation Toolkit☆105Jul 5, 2024Updated last year