Alternatives and similar repositories for dock-prep

Users that are interested in dock-prep are comparing it to the libraries listed below

• DrugBud-Suite / CADD_Vault
  ☆49Updated 2 months ago
• HoffOskar / ML_From_Scratch
  Creating machine learning algorithms from scratch
  ☆18Updated last month
• Gervasiolab / OpenBPMD
  ☆65Updated last year
• mqcomplab / bitbirch
  BitBIRCH clustering algorithm
  ☆76Updated last week
• freeenergylab / FEP-SPell-ABFE
  FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery
  ☆63Updated 4 months ago
• PatWalters / TS
  Thompson Sampling
  ☆67Updated 3 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.
  ☆49Updated 2 months ago
• durrantlab / gypsum_dl
  Open-source tool to generate 3D-ready small molecules for virtual screening
  ☆54Updated this week
• durrantlab / dimorphite_dl
  Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range
  ☆30Updated this week
• durrantlab / autogrow4
  AutoGrow4 is an open-source program for semi-automated computer-aided drug discovery. It uses a genetic algorithm to evolve predicted lig…
  ☆43Updated this week
• molecularinformatics / roshambo
  ☆80Updated 9 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…
  ☆55Updated last month
• durrantlab / deepfrag
  DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…
  ☆25Updated last year
• MolSSI-Education / iqb-2025
  This repository contains notebooks for the workshop Python for Cheminformatics-Driven Molecular Docking held on May 1, 2025 in collaborat…
  ☆77Updated last month
• forlilab / cosolvkit
  CosolvKit is a versatile tool for cosolvent MD preparation and analysis
  ☆24Updated 3 weeks ago
• lmmpf / PyAutoFEP
  PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
  ☆77Updated last year
• fhh2626 / BFEE2
  binding free energy estimator 2
  ☆118Updated last week
• callumjd / AMBER-Membrane_protein_tutorial
  Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen
  ☆63Updated last year
• yboulaamane / cdd-toolbox
  A curated list of tools and servers for computer-aided drug design and discovery.
  ☆27Updated 2 weeks ago
• sulfierry / free_energy_landscape
  The Free Energy Landscape Analysis tool offers a comprehensive suite for analyzing and visualizing the free energy landscape derived from…
  ☆21Updated 3 months ago
• uibcdf / OpenPharmacophore
  An open library to work with pharmacophores.
  ☆45Updated last year
• THGLab / HiQBind
  Workflow to clean up and fix structural problems in protein-ligand binding datasets
  ☆45Updated 3 weeks ago
• IFMlab / ChemFlow
  Computational Chemistry Workflows
  ☆53Updated 2 years ago
• MolecularAI / Lib-INVENT
  ☆56Updated 2 years ago
• CDDLeiden / QSPRpred
  A tool for creating Quantitative Structure Property/Activity Relationship (QSPR/QSAR) models.
  ☆69Updated 2 months ago
• brueckna2020 / MDFit
  Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics
  ☆18Updated last year
• czodrowskilab / Machine-learning-meets-pKa
  ☆73Updated last year
• Aouidate / Chemoinformatics-compiliation
  In the current repository, I will try to compile the sources of Cheminformatics that can be helpful for anyone that needs them
  ☆32Updated 3 months ago
• schrodinger / public_binding_free_energy_benchmark
  The public versio
  ☆54Updated last year
• meddwl / psearch
  3D ligand-based pharmacophore modeling
  ☆48Updated 3 weeks ago