Alternatives and similar repositories for reeds

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

• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆33Updated last year
• MobleyLab / alchemical-setup
  ☆16Updated 8 years ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• 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
• drazen-petrov / SMArt
  ☆30Updated last week
• 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 8 months ago
• arwalkerlab / AutoParams
  ☆28Updated last year
• hutchisonlab / QupKake
  Machine Learning model for molecular micro-pKa prediction
  ☆46Updated last year
• pfizer-opensource / TorsionNet
  A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM
  ☆39Updated 2 years ago
• cbc-univie / transformato
  Set up relative free energy calculations using a common scaffold
  ☆24Updated 3 months ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated last month
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆31Updated last month
• MobleyLab / SeparatedTopologies
  Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).
  ☆28Updated last year
• choderalab / qmlify
  ☆44Updated 3 years ago
• rinikerlab / restraintmaker
  Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…
  ☆19Updated 3 years ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆30Updated 3 years ago
• RPirie96 / RGMolSA
  ☆35Updated last year
• essex-lab / grand
  A Python module for carrying out GCMC insertions and deletions of water molecules in OpenMM.
  ☆72Updated 2 years ago
• keisuke-yanagisawa / exprorer
  EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation
  ☆11Updated 3 years ago
• DingGroup / BayesMBAR
  Bayesian Multistate Bennett Acceptance Ratio Method
  ☆15Updated last month
• OpenFreeEnergy / kartograf
  This package contains tools for setting up hybrid-topology FE calculations
  ☆32Updated this week
• callumjd / AMBER-Umbrella_COM_restraint_tutorial
  Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane
  ☆38Updated 2 years ago
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆34Updated 2 months ago
• OpenFreeEnergy / IndustryBenchmarks2024
  Repository for the 2024 OpenFE industry benchmark efforts
  ☆25Updated 2 months ago
• HITS-MCM / tauRAMD
  Computation of the drug-target relative residence times from RAMD simulations
  ☆18Updated last year
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆42Updated last week
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆18Updated 2 years ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 3 years ago
• molecularinformatics / roshambo2
  ☆35Updated 3 months ago