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

• choderalab / qmlify
  ☆44Updated 3 years ago
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• choderalab / espaloma-charge
  Standalone charge assignment from Espaloma framework.
  ☆45Updated 2 months ago
• alchemistry / alchemical-best-practices
  Best practice document for alchemical free energy calculations going to livecoms journal
  ☆80Updated last week
• dkoes / md-scripts
  A collections of scripts for working molecular dynamics simulations
  ☆44Updated 4 months ago
• cdsgroup / resp
  A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4
  ☆34Updated 5 months ago
• OpenFreeEnergy / cinnabar
  Package for consistent reporting of relative free energy results
  ☆40Updated last month
• protocaller / ProtoCaller
  Full automation of relative protein-ligand binding free energy calculations in GROMACS
  ☆46Updated 4 years ago
• drazen-petrov / SMArt
  ☆30Updated 2 weeks ago
• GilsonLabUCSD / pAPRika
  Advanced toolkit for binding free energy calculations
  ☆33Updated 3 months ago
• openmm / openmm_workshops
  ☆39Updated last year
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 3 months ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆33Updated 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
• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆28Updated last year
• insilichem / ommprotocol
  A command line application to launch molecular dynamics simulations with OpenMM
  ☆40Updated 3 years ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated last month
• OpenFreeEnergy / IndustryBenchmarks2024
  Repository for the 2024 OpenFE industry benchmark efforts
  ☆25Updated 2 months ago
• OpenFreeEnergy / feflow
  Recipes and protocols for molecular free energy calculations using the openmmtools/perses and Open Free Energy toolkits
  ☆15Updated 2 weeks ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆30Updated 3 years ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• openforcefield / openff-recharge
  An automated framework for generating optimized partial charges for molecules
  ☆39Updated 2 weeks ago
• openforcefield / openff-sage
  Scripts, inputs and the results generated as part of the training the Sage line of OpenFF force fields.
  ☆21Updated 5 months 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.
  ☆58Updated 8 months ago
• OpenFreeEnergy / ExampleNotebooks
  Notebooks demonstrating how to do simple tasks related to free energy calculations.
  ☆55Updated this week
• giovanni-bolcato / deepFMPOv3D
  Implementation of Shape and Electrostatic similarity metric in deepFMPO.
  ☆45Updated 3 years ago
• maxscheurer / pycontact
  Analysis of non-covalent interactions in MD trajectories
  ☆65Updated 11 months ago
• lilyminium / psiresp
  RESP with inter- and intra-molecular constraints in Psi4.
  ☆32Updated 2 years ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆29Updated 2 years ago