PDBFixer fixes problems in PDB files
☆626Oct 30, 2025Updated 4 months ago
Alternatives and similar repositories for pdbfixer
Users that are interested in pdbfixer are comparing it to the libraries listed below
Sorting:
- Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Schake,…☆649Oct 30, 2025Updated 4 months ago
- CHARMM and AMBER forcefields for OpenMM (with small molecule support)☆350Jan 6, 2026Updated last month
- A Python Package for Protein Dynamics Analysis☆529Feb 13, 2026Updated 2 weeks ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆336Feb 16, 2026Updated last week
- A dependency-free cross-platform swiss army knife for PDB files.☆444Feb 3, 2026Updated 3 weeks ago
- Interaction Fingerprints for protein-ligand complexes and more☆477Feb 22, 2026Updated last week
- OpenMM is a toolkit for molecular simulation using high performance GPU code.☆1,803Updated this week
- PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.☆166Feb 16, 2026Updated 2 weeks ago
- An open library for the analysis of molecular dynamics trajectories☆700Feb 12, 2026Updated 2 weeks ago
- Plausibility checks for generated molecule poses.☆355Feb 9, 2026Updated 3 weeks ago
- P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.☆393Updated this week
- A deep learning framework for molecular docking☆860Dec 23, 2025Updated 2 months ago
- Parameter/topology editor and molecular simulator☆448Jan 12, 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…☆442Sep 9, 2024Updated last year
- Protein-protein, protein-peptide and protein-DNA docking framework based on the GSO algorithm☆380Sep 16, 2025Updated 5 months ago
- A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.☆315Jan 7, 2026Updated last month
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆169Feb 12, 2026Updated 2 weeks ago
- A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files☆180Oct 10, 2019Updated 6 years ago
- AutoDock Vina☆924Updated this week
- MDAnalysis is a Python library to analyze molecular dynamics simulations.☆1,540Feb 19, 2026Updated last week
- An application for configuring and running simulations with OpenMM☆76Oct 30, 2025Updated 4 months ago
- Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking☆1,440May 2, 2025Updated 10 months ago
- MoleculeKit: Your favorite molecule manipulation kit☆235Updated this week
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆216Jul 29, 2024Updated last year
- The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation avai…☆382Feb 17, 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.☆297Dec 8, 2025Updated 2 months ago
- Jupyter widget to interactively view molecular structures and trajectories☆913Feb 2, 2026Updated last month
- C-library for calculating Solvent Accessible Surface Areas☆178Nov 15, 2025Updated 3 months ago
- MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.☆731Jun 19, 2024Updated last year
- Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design☆664Feb 12, 2026Updated 2 weeks ago
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆220Jan 27, 2026Updated last month
- End-To-End Molecular Dynamics (MD) Engine using PyTorch☆685Jan 7, 2026Updated last month
- Reduce - tool for adding and correcting hydrogens in PDB files☆168Jan 5, 2026Updated last month
- Making Protein Design accessible to all via Google Colab!☆886Dec 8, 2025Updated 2 months ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆245Feb 18, 2026Updated last week
- Interface for AutoDock, molecule parameterization☆340Updated this week
- Collected scripts for Pymol☆515Feb 7, 2026Updated 3 weeks ago
- Python interface of cpptraj☆188Jan 20, 2026Updated last month
- An interoperable Python framework for biomolecular simulation.☆146Updated this week