Alternatives and similar repositories for protein-ligand-benchmark-livecoms

Users that are interested in protein-ligand-benchmark-livecoms are comparing it to the libraries listed below

• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• choderalab / qmlify
  ☆44Updated 3 years ago
• GilsonLabUCSD / pAPRika
  Advanced toolkit for binding free energy calculations
  ☆33Updated 2 months ago
• cdsgroup / resp
  A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4
  ☆34Updated 5 months ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• alchemistry / alchemical-best-practices
  Best practice document for alchemical free energy calculations going to livecoms journal
  ☆79Updated last week
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 3 months ago
• giovanni-bolcato / deepFMPOv3D
  Implementation of Shape and Electrostatic similarity metric in deepFMPO.
  ☆45Updated 3 years ago
• drazen-petrov / SMArt
  ☆30Updated last week
• protocaller / ProtoCaller
  Full automation of relative protein-ligand binding free energy calculations in GROMACS
  ☆45Updated 4 years ago
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆44Updated 3 months ago
• OpenFreeEnergy / cinnabar
  Package for consistent reporting of relative free energy results
  ☆40Updated last week
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆43Updated last month
• openforcefield / openff-recharge
  An automated framework for generating optimized partial charges for molecules
  ☆39Updated last month
• rdkit / shape-it
  Updated version of Silicos-it's shape-based alignment tool
  ☆43Updated last month
• lilyminium / psiresp
  RESP with inter- and intra-molecular constraints in Psi4.
  ☆32Updated 2 years ago
• openforcefield / ccpbiosim-2023
  Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week
  ☆31Updated 2 years ago
• Albert-Lau-Lab / tactics_protein_analysis
  ☆17Updated last year
• otayfuroglu / deepQM
  ☆28Updated 6 months ago
• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆28Updated 11 months ago
• qusers / Q6
  Q6 Repository -- EVB, FEP and LIE simulator.
  ☆35Updated 2 years ago
• mms-fcul / PypKa
  A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
  ☆61Updated last year
• OpenFreeEnergy / IndustryBenchmarks2024
  Repository for the 2024 OpenFE industry benchmark efforts
  ☆25Updated last month
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• OpenFreeEnergy / ExampleNotebooks
  Notebooks demonstrating how to do simple tasks related to free energy calculations.
  ☆55Updated 2 weeks ago
• bigginlab / ABFE_workflow
  This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.
  ☆57Updated 7 months ago
• choderalab / pymbar-examples
  Examples of applications of pymbar to various problems in simulation and experiment
  ☆23Updated 10 years ago
• OpenFreeEnergy / kartograf
  This package contains tools for setting up hybrid-topology FE calculations
  ☆32Updated last month
• MobleyLab / benchmarkff
  Compare optimized geometries and energies from various force fields with respect to a QM reference.
  ☆13Updated 4 years ago
• rdkit / UGM_2020
  Materials from the (virtual) 2020 RDKit UGM
  ☆52Updated 5 years ago