deGrootLab / pmx

Related projects ⓘ

Alternatives and complementary repositories for pmx

• MCompChem / fep-benchmark
  Benchmark set for relative free energy calculations.
  ☆99Updated 6 months ago
• fhh2626 / BFEE2
  binding free energy estimator 2
  ☆108Updated 2 weeks ago
• lmmpf / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆74Updated last year
• wlsong / PyLipID
  A python toolkit for analysing membrane protein-lipid interactions.
  ☆60Updated last year
• cole-group / FEgrow
  An Open-Source Molecular Builder and Free Energy Preparation Workflow
  ☆119Updated last week
• 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…
  ☆95Updated 2 weeks ago
• luancarvalhomartins / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆165Updated last year
• dseeliger / pmx
  Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
  ☆57Updated 3 years ago
• tdudgeon / simple-simulate-complex
  Simple protein-ligand complex simulation with OpenMM
  ☆73Updated last year
• MolecularAI / DockStream
  DockStream: A Docking Wrapper to Enhance De Novo Molecular Design
  ☆108Updated last year
• MiaoLab20 / gamd-openmm
  Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…
  ☆70Updated 5 months ago
• Gallicchio-Lab / AToM-OpenMM
  OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method
  ☆120Updated 3 weeks ago
• Electrostatics / pdb2pqr
  PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
  ☆130Updated last week
• maccallumlab / martini_openmm
  ☆49Updated last year
• marrink-lab / vermouth-martinize
  Describe and apply transformation on molecular structures and topologies
  ☆99Updated this week
• callumjd / AMBER-Membrane_protein_tutorial
  Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
  ☆53Updated 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…
  ☆178Updated last month
• PatWalters / chem_tutorial
  ☆89Updated 2 years ago
• isayevlab / Auto3D_pkg
  Auto3D generates low-energy conformers from SMILES/SDF
  ☆149Updated 3 months ago
• CCPBioSim / fesetup
  A tool for setting up free energy simulations.
  ☆34Updated 2 years ago
• CharlesHahn / DuIvy
  some scripts for analysis of MD and CADD. And some tutorials.
  ☆52Updated 3 months ago
• hesther / espsim
  Scoring of shape and ESP similarity with RDKit
  ☆206Updated last year
• CharlesHahn / DuIvyTools
  A Tool to process and visualize the results of molecular dynamics simulations(GROMACS).
  ☆62Updated 3 months ago
• matteoferla / Fragmenstein
  Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
  ☆181Updated last week
• IanAWatson / Lilly-Medchem-Rules
  Implementation of Lilly Medchem Rules - J Med Chem 2012
  ☆84Updated last month
• maccallumlab / meld
  Modeling with limited data
  ☆54Updated last week
• openforcefield / protein-ligand-benchmark
  Protein-Ligand Benchmark Dataset for Free Energy Calculations
  ☆150Updated 3 months ago
• huichenggong / Learning-Computation-with-Chenggong
  ☆39Updated 4 months ago
• jalemkul / gmx_tutorials_livecoms
  LiveCoMS GROMACS Tutorials Paper
  ☆109Updated 5 years ago
• cosconatilab / PyRMD
  AI-powered Virtual Screening
  ☆83Updated last year