Alternatives and similar repositories for pdb2pqr:

Users that are interested in pdb2pqr are comparing it to the libraries listed below

• fhh2626 / BFEE2
  binding free energy estimator 2
  ☆113Updated last week
• deGrootLab / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆143Updated 3 weeks ago
• matteoferla / Fragmenstein
  Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
  ☆187Updated 3 months ago
• Electrostatics / apbs
  Software for biomolecular electrostatics and solvation calculations
  ☆102Updated 7 months ago
• luancarvalhomartins / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆188Updated last year
• GHeinzelmann / BAT.py
  The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy (ABFE) and relative binding free energy (RB…
  ☆197Updated 2 months ago
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆112Updated this week
• rlabduke / reduce
  Reduce - tool for adding and correcting hydrogens in PDB files
  ☆141Updated 3 weeks ago
• forlilab / Meeko
  Interface for AutoDock, molecule parameterization
  ☆250Updated this week
• PatWalters / useful_rdkit_utils
  Some useful RDKit functions
  ☆169Updated last month
• Valdes-Tresanco-MS / AutoDockTools_py3
  Python3 translation of AutoDockTools
  ☆113Updated 11 months ago
• tdudgeon / simple-simulate-complex
  Simple protein-ligand complex simulation with OpenMM
  ☆84Updated last year
• getcontacts / getcontacts
  Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation
  ☆112Updated last year
• lmmpf / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆75Updated last year
• CharlesHahn / DuIvyTools
  A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).
  ☆72Updated 8 months ago
• wolberlab / OpenMMDL
  Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
  ☆127Updated this week
• MiaoLab20 / gamd-openmm
  Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…
  ☆81Updated last week
• isayevlab / Auto3D_pkg
  Auto3D generates low-energy conformers from SMILES/SDF
  ☆167Updated last month
• hesther / espsim
  Scoring of shape and ESP similarity with RDKit
  ☆214Updated last month
• MolSSI-Education / iqb-2025
  ☆13Updated this week
• AstexUK / ESP_DNN
  A Graph-Convolutional Deep Neural Network for predicting electrostatic potential surfaces
  ☆88Updated 2 years ago
• volkamerlab / opencadd
  A Python library for structural cheminformatics
  ☆99Updated this week
• MCompChem / fep-benchmark
  Benchmark set for relative free energy calculations.
  ☆105Updated 11 months ago
• alanwilter / acpype
  OFFICIAL: AnteChamber PYthon Parser interfacE
  ☆226Updated 3 months ago
• dptech-corp / Uni-GBSA
  An automatic workflow to perform MM/GB(PB)SA calculations from force field building, and structure optimization to free energy calculatio…
  ☆105Updated 6 months ago
• DrrDom / pmapper
  3D pharmacophore signatures and fingerprints
  ☆103Updated 4 months ago
• Gallicchio-Lab / AToM-OpenMM
  OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
  ☆132Updated last month
• maccallumlab / martini_openmm
  ☆54Updated 2 years ago
• maccallumlab / meld
  Modeling with limited data
  ☆57Updated 5 months ago
• openforcefield / protein-ligand-benchmark
  Protein-Ligand Benchmark Dataset for Free Energy Calculations
  ☆173Updated 9 months ago