Electrostatics / pdb2pqrLinks
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
☆156Updated 7 months ago
Alternatives and similar repositories for pdb2pqr
Users that are interested in pdb2pqr are comparing it to the libraries listed below
Sorting:
- Software for biomolecular electrostatics and solvation calculations☆114Updated last year
- PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods☆194Updated 2 years ago
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆160Updated 2 months ago
- Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation☆130Updated 2 years ago
- Reduce - tool for adding and correcting hydrogens in PDB files☆156Updated 5 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…☆211Updated 2 weeks ago
- OFFICIAL: AnteChamber PYthon Parser interfacE☆236Updated 4 months ago
- binding free energy estimator 2☆131Updated 3 weeks ago
- Describe and apply transformation on molecular structures and topologies☆125Updated last week
- Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse☆198Updated 9 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆149Updated this week
- ☆131Updated 6 years ago
- C-library for calculating Solvent Accessible Surface Areas☆161Updated 3 months ago
- Simple protein-ligand complex simulation with OpenMM☆90Updated 2 years ago
- PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.☆144Updated 8 months ago
- Interface for AutoDock, molecule parameterization☆304Updated last week
- Scoring of shape and ESP similarity with RDKit☆227Updated 2 months ago
- Python3 translation of AutoDockTools☆128Updated last year
- Python package to run molecular dynamics simulation of a protein-ligand complex in a single line of code.☆167Updated last month
- A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).☆82Updated last year
- clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)☆119Updated last year
- Protein-Ligand Benchmark Dataset for Free Energy Calculations☆203Updated last year
- Auto3D generates low-energy conformers from SMILES/SDF☆181Updated 5 months ago
- PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.☆321Updated last year
- gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.☆278Updated 3 months ago
- OpenMM tutorial for the MSBS course☆177Updated last week
- An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…☆120Updated 11 months ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆29Updated last week
- Trusted force field files for gromacs☆61Updated 11 months ago
- A Python package for molecular docking with an extensive, highly-curated dataset and a set of realistic benchmark tasks for drug discover…☆175Updated 2 weeks ago