Alternatives and similar repositories for PARENT:

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

• 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
  ☆30Updated last year
• huichenggong / Learning-Computation-with-Chenggong
  ☆39Updated 8 months ago
• emleddin / research-scripts
  Different run and analysis scripts as described in the research guides.
  ☆13Updated 2 years 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.
  ☆46Updated 4 months ago
• dspoel / remd-temperature-generator
  Temperature generator for Replica Exchange MD simulations
  ☆27Updated 2 years ago
• freeenergylab / FEP-SPell-ABFE
  FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  ☆50Updated 2 months ago
• MottaStefano / PathDetect-SOM
  A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)
  ☆10Updated 3 years ago
• UCL-CCS / TIES_MD
  Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
  ☆32Updated last year
• ykhdrew / qMSM_tutorial
  A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison
  ☆15Updated last year
• bioexcel / gromacs-2022-cp2k-tutorial
  Sample inputs and tutorial for GROMACS-2022/CP2K QMMM interface
  ☆35Updated 3 years ago
• NNairIITK / Enhanced_Sampling_Methods_Tutorials
  Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..
  ☆44Updated 4 years ago
• Gervasiolab / OpenBPMD
  ☆55Updated last year
• arwalkerlab / AutoParams
  ☆26Updated last year
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆40Updated last year
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆20Updated 2 years ago
• HITS-MCM / gromacs-ramd
  Random Acceleration Molecular Dynamics in GROMACS
  ☆36Updated 8 months ago
• GHeinzelmann / GHOAT.py
  The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.
  ☆17Updated 7 months ago
• federico-fogolari / pdb2entropy
  Entropy from PDB conformational ensembles
  ☆7Updated 11 months ago
• dooo12332 / AlphaTraj
  Pocket dynamics analysis tool
  ☆12Updated this week
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last week
• otayfuroglu / deepQM
  ☆27Updated 9 months ago
• delemottelab / InfleCS-free-energy-clustering-tutorial
  Python tutorial for estimating and clustering free energy landscapes with InfleCS.
  ☆28Updated 2 years ago
• callumjd / AMBER-Membrane_protein_tutorial
  Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
  ☆58Updated last year
• forlilab / cosolvkit
  CosolvKit is a versatile tool for cosolvent MD preparation and analysis
  ☆23Updated last month
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆24Updated last month
• IFMlab / ChemFlow
  Computational Chemistry Workflows
  ☆54Updated 2 years ago
• netscianalysis / netsci
  ☆13Updated 3 months ago
• JecaTosovic / WaterNetworkAnalysis
  Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis
  ☆17Updated 4 months ago
• CCPBioSim / fesetup
  A tool for setting up free energy simulations.
  ☆35Updated 2 years ago