Alternatives and similar repositories for shepherd

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

• keiradams / SQUID
  Official implementation of "Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design"
  ☆67Updated 11 months ago
• camlab-ethz / GEMS
  Protein-Ligand Binding Affinity Prediction with GNN and Transfer Learning From Protein Language Models
  ☆66Updated last month
• THGLab / LP-PDBBind
  ☆57Updated 4 months ago
• dptech-corp / Uni-pKa
  The official repository of Uni-pKa
  ☆84Updated 7 months ago
• THGLab / HiQBind
  Workflow to clean up and fix structural problems in protein-ligand binding datasets
  ☆59Updated last week
• MolecularAI / Lib-INVENT
  ☆58Updated 2 years ago
• MatthewMasters / EDM-Dock
  ☆32Updated 2 years ago
• ghiander / novana
  Cheminformatics tool that extends the decomposition of molecules into Bemis-Murcko frameworks.
  ☆52Updated 8 months ago
• DrugBud-Suite / DockM8
  All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.
  ☆50Updated 2 weeks ago
• SeonghwanSeo / PharmacoNet
  Official Github for "PharmacoNet: deep learning-guided pharmacophore modeling for ultra-large-scale virtual screening" (Chemical Science)
  ☆81Updated 4 months ago
• MorganCThomas / SMILES-RNN
  Repository for SMILES-based RNNs for reinforcement learning-based de novo molecule generation
  ☆64Updated 2 weeks ago
• Xundrug / MolGpKa
  The graph-convolutional neural network for pka prediction
  ☆91Updated last year
• schrodinger / public_binding_free_energy_benchmark
  The public versio
  ☆67Updated 2 years ago
• tiejundong / FlexPose
  FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.
  ☆54Updated last year
• coleygroup / shepherd-score
  Interaction profile extraction, scoring, alignment and evaluation of ShEPhERD. [ICLR 2025]
  ☆30Updated last month
• Brian-hongyan / 3D-MCTS
  3D-MCTS: A general structure-based molecule generation method with MCTS.
  ☆44Updated last year
• VicFisher / DiffPhore
  Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping
  ☆43Updated 5 months ago
• molecularinformatics / roshambo
  ☆90Updated last year
• drorlab / combind
  Integrated physics-based and ligand-based modeling.
  ☆66Updated 3 weeks ago
• ACE-KAIST / DeepICL
  Official Github for "3D Molecular Generative Framework for Interaction-guided Drug Design" (Nature Communications)
  ☆63Updated last year
• Laboratoire-de-Chemoinformatique / Synt-On
  Open-source tool for synthons-based library design.
  ☆83Updated 10 months ago
• Carlssonlab / conformalpredictor
  Machine learning accelerated docking screens
  ☆65Updated 10 months ago
• durrantlab / dimorphite_dl
  Adds or removes hydrogen atoms to achieve the appropriate molecular protonation state for a user-specified pH range
  ☆50Updated 3 months ago
• zchwang / DeepRMSD-Vina_Optimization
  DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.
  ☆42Updated last year
• oxpig / MolSnapper
  ☆52Updated 6 months ago
• bpmunson / polygon
  POLYGON VAE For de novo Polypharmacology
  ☆40Updated 8 months ago
• ale94mleon / BindFlow
  A snakemake-based workflow for FEP and MM(PB/GB)SA calculations with GROMACS
  ☆118Updated this week
• stonewiseAIDrugDesign / Lingo3DMol
  ☆60Updated last year
• plainerman / DiffDock-Pocket
  Implementation of DiffDock-Pocket: Diffusion for Pocket-Level Docking with Side Chain Flexibility
  ☆34Updated last year
• oxpig / DEVELOP
  ☆56Updated last year