Electrostatics / pdb2pqrLinks
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
☆146Updated 3 months ago
Alternatives and similar repositories for pdb2pqr
Users that are interested in pdb2pqr are comparing it to the libraries listed below
Sorting:
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆149Updated 2 weeks ago
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆189Updated last year
- Software for biomolecular electrostatics and solvation calculations☆102Updated 8 months ago
- binding free energy estimator 2☆116Updated last week
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆188Updated 4 months ago
- Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation☆116Updated last year
- This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…☆77Updated last month
- The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…☆198Updated 3 months ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆144Updated 2 weeks ago
- Describe and apply transformation on molecular structures and topologies☆112Updated 2 weeks ago
- Some useful RDKit functions☆183Updated 3 weeks ago
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆171Updated last month
- A Python library for structural cheminformatics☆100Updated last month
- Auto3D generates low-energy conformers from SMILES/SDF☆171Updated last week
- Simple protein-ligand complex simulation with OpenMM☆85Updated last year
- Benchmark set for relative free energy calculations.☆105Updated last year
- Scoring of shape and ESP similarity with RDKit☆216Updated 2 months ago
- DockStream: A Docking Wrapper to Enhance De Novo Molecular Design☆119Updated 2 years ago
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆109Updated 6 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆128Updated this week
- A python toolkit for analysing membrane protein-lipid interactions.☆63Updated 2 years ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆81Updated last month
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆76Updated last year
- Python3 translation of AutoDockTools☆118Updated last year
- ☆121Updated 6 years ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆228Updated 4 months ago
- A script to run structural alerts using the RDKit and ChEMBL☆143Updated last year
- Interface for AutoDock, molecule parameterization☆255Updated 3 weeks ago
- OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method☆134Updated this week
- PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.☆130Updated 2 months ago