Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction
☆88Oct 6, 2025Updated 5 months ago
Alternatives and similar repositories for PhysDock
Users that are interested in PhysDock are comparing it to the libraries listed below
Sorting:
- SurfDock is a Surface-Informed Diffusion Generative Model for Reliable and Accurate Protein-ligand Complex Prediction☆233Sep 29, 2025Updated 5 months ago
- ☆16Sep 15, 2025Updated 5 months ago
- Neural Iterative Selection-Expansion using LigandMPNN/LASErMPNN and Boltz-2x☆32Feb 12, 2026Updated 3 weeks ago
- SableBind is an open-source framework dedicated to predicting protein-ligand binding affinity☆13Feb 6, 2025Updated last year
- GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data☆26Dec 5, 2025Updated 3 months ago
- All-Atom (Including Hydrogen!) Ligand-Conditioned Protein Sequence Design & Sidechain Packing GNN☆27Updated this week
- An accurate and trainable end-to-end protein-ligand docking framework☆127Mar 24, 2025Updated 11 months ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Feb 25, 2026Updated last week
- An open-source platform for developing protein models beyond AlphaFold.☆12Jul 15, 2025Updated 7 months ago
- Diffusion model based protein-ligand flexible docking method☆116Oct 30, 2024Updated last year
- ☆114Jul 18, 2025Updated 7 months ago
- Implementation of NeurIPS24 paper "Generalized Protein Pocket Generation with Prior-Informed Flow Matching"☆19May 15, 2025Updated 9 months ago
- Versatile Molecular Editing via Multimodal and Group-optimized Generative Learning☆24May 22, 2025Updated 9 months ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆61Jan 30, 2026Updated last month
- Plugin for folding sequences directly in PyMOL☆116Aug 4, 2025Updated 7 months ago
- Protein-ligand structure prediction☆239Jul 31, 2025Updated 7 months ago
- NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model☆325Oct 6, 2025Updated 5 months ago
- ☆134Aug 8, 2024Updated last year
- Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding☆38Nov 25, 2025Updated 3 months ago
- P2DFlow: A Protein Ensemble Generative Model with SE(3) Flow Matching☆44May 22, 2025Updated 9 months ago
- Official repo of "CarsiDock: a deep learning paradigm for accurate protein–ligand docking and screening based on large-scale pre-training…☆111Aug 13, 2025Updated 6 months ago
- A geometric flow matching model for generative protein-ligand docking and affinity prediction. (ISMB 2025)☆126Sep 3, 2025Updated 6 months ago
- Implementation for SuperWater☆41Jan 9, 2026Updated 2 months ago
- This Code is for Fragment-wise 3D Structure-based Molecular Generation with Reliable Geometry☆33Mar 24, 2025Updated 11 months ago
- Disordered protein ensemble prediction☆12Feb 19, 2026Updated 2 weeks ago
- Knowledge-Guided Diffusion Model for 3D Ligand-Pharmacophore Mapping☆47Jan 28, 2026Updated last month
- ☆74Feb 13, 2026Updated 3 weeks ago
- ☆46Dec 30, 2025Updated 2 months ago
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆164Mar 1, 2026Updated last week
- Protein-Ligand Binding Affinity Prediction with GNN and Transfer Learning From Protein Language Models☆77Mar 2, 2026Updated last week
- Official repository for DiffPepBuilder and DiffPepDock tools☆119Oct 24, 2025Updated 4 months ago
- A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD☆15Updated this week
- ESMDynamic repo☆22Feb 25, 2026Updated last week
- Fold Conditioned protein design pipeline based on AF2Multimer Hallucination☆49Dec 2, 2025Updated 3 months ago
- PLACER is graph neural network for local prediction of protein-ligand conformational ensembles.☆229Nov 5, 2025Updated 4 months ago
- DFMDock (Denoising Force Matching Dock), a diffusion model that unifies sampling and ranking within a single framework.☆53Jul 22, 2025Updated 7 months ago
- composite-objective protein design☆265Updated this week
- Multi-domain Distribution Learning for De Novo Drug Design☆144Jan 26, 2026Updated last month
- DyNoPy☆11Sep 5, 2024Updated last year