Alternatives and similar repositories for PRIME

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

• 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.
  ☆56Updated 7 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year
• Gervasiolab / OpenBPMD
  ☆68Updated 2 years ago
• forlilab / cosolvkit
  CosolvKit is a versatile tool for cosolvent MD preparation and analysis
  ☆26Updated last week
• 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
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆33Updated last month
• IFMlab / ChemFlow
  Computational Chemistry Workflows
  ☆55Updated 3 years ago
• IAlibay / MDRestraintsGenerator
  Python code for generating Boresch restraints from MD simulations
  ☆22Updated 2 weeks ago
• rinikerlab / reeds
  This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…
  ☆32Updated 4 months ago
• RPirie96 / RGMolSA
  ☆35Updated last year
• ci-lab-cz / streamd
  Fully automated high-throughput MD pipeline
  ☆81Updated last month
• freeenergylab / FEP-SPell-ABFE
  FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  ☆74Updated 9 months ago
• ale94mleon / moldrug
  moldrug (AKA mouse) is a Python package for drug-oriented optimization on the chemical space ​
  ☆37Updated last month
• 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
• dlukauskis / funnel_maker
  Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.
  ☆15Updated 2 years ago
• Gallicchio-Lab / openmm-atmmetaforce-plugin
  An OpenMM plugin that implements the Alchemical Transfer Potential
  ☆39Updated 2 years ago
• schrodinger / public_binding_free_energy_benchmark
  The public versio
  ☆67Updated 2 years ago
• Exscientia / plif_validity
  Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"
  ☆19Updated last year
• oxpig / MolSnapper
  ☆51Updated 5 months ago
• sbhakat / AF-cryptic-pocket
  Cryptic pocket prediction using AlphaFold 2
  ☆24Updated 2 years ago
• brueckna2020 / MDFit
  Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
  ☆19Updated last year
• seekrcentral / seekr2
  Simulation-Enabled Estimation of Kinetic Rates - Version 2
  ☆32Updated last month
• 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.
  ☆20Updated 5 months ago
• quantaosun / Dock-MD-FEP
  Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…
  ☆59Updated 6 months ago
• callumjd / AMBER-Membrane_protein_tutorial
  Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
  ☆68Updated 2 years ago
• netscianalysis / netsci
  ☆14Updated 10 months ago
• pablo-arantes / ParametrizANI
  Free Parametrization for Small Molecules
  ☆47Updated 3 weeks ago
• limresgrp / FMAP_v1
  Codes to use funnel-metadynamics and funnel metadynamics automated protocol
  ☆30Updated 3 years ago
• 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
  ☆37Updated 2 years ago
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆28Updated last week