Alternatives and similar repositories for AGDIFF

Users that are interested in AGDIFF 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.
  ☆32Updated last year
• forlilab / waterkit
  Tool to predict water molecules placement and energy in ligand binding sites
  ☆28Updated last week
• nobiastx / diffusion-conformer
  Diffusion-based molecule conformer generation
  ☆41Updated last year
• michellab / a3fe
  Automated Adaptive Absolute alchemical Free Energy calculator
  ☆105Updated this week
• OpenBioSim / biosimspace_tutorials
  A tutorials suite for BioSimSpace.
  ☆25Updated 3 months ago
• mqcomplab / PRIME
  protein structure prediction with precision
  ☆19Updated last year
• dptech-corp / Uni-pKa
  The official repository of Uni-pKa
  ☆66Updated 4 months ago
• zchwang / IGModel
  This is the first model that can simultaneously predict the RMSD of the ligand docking pose and the binding strength against the target.
  ☆19Updated 7 months ago
• MikkelDA / COBY
  COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3
  ☆40Updated this week
• rinikerlab / GNNImplicitSolvent
  Implicit Solvent Approach Based on Generalised Born and Transferable Graph Neural Networks for Molecular Dynamics Simulations
  ☆50Updated 4 months ago
• schwallergroup / augmented_memory
  Augmented Memory and Beam Enumeration implementation
  ☆25Updated last year
• 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.
  ☆19Updated 3 months ago
• Exscientia / plif_validity
  Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"
  ☆18Updated 10 months ago
• molML / RUSH
  ☆16Updated 6 months ago
• pablo-arantes / ParametrizANI
  Free Parametrization for Small Molecules
  ☆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.
  ☆50Updated 5 months ago
• luost26 / ChemProjector
  Projecting Molecules into Synthesizable Chemical Spaces (ICML 2024)
  ☆43Updated 3 weeks ago
• oxpig / AEV-PLIG
  ☆22Updated 6 months ago
• adalke / mmpdb
  A package to identify matched molecular pairs and use them to predict property changes.
  ☆24Updated last year
• oxpig / MolSnapper
  ☆50Updated 3 months ago
• ashipiling / GPT_3DSMILES
  ☆30Updated this week
• durrantlab / deepfrag
  DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…
  ☆26Updated 2 months ago
• BioinfoMachineLearning / GCDM-SBDD
  A geometry-complete diffusion generative model (GCDM) for structure-based drug design (Nature CommsChem)
  ☆19Updated 9 months ago
• seekrcentral / seekr2
  Simulation-Enabled Estimation of Kinetic Rates - Version 2
  ☆32Updated last month
• OdinZhang / FragGen
  This Code is for Fragment-wise 3D Structure-based Molecular Generation with Reliable Geometry
  ☆27Updated 5 months ago
• litfsindt / LIT-SpaceDock
  ☆16Updated last year
• arwalkerlab / AutoParams
  ☆28Updated last year
• MarcMoesser / Protein-Ligand-Interaction-Graphs
  ☆40Updated 2 years ago
• Academich / reagents
  Reagent prediction with Molecular Transformer. Improvement of data for reaction product prediction in a self-supervised fashion.
  ☆27Updated 10 months ago
• michellab / BioSimSpaceTutorials
  ☆25Updated last year