FlexPose, a framework for AI-based flexible modeling of protein-ligand binding pose.
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Dec 27, 2023 - Python
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protein-ligand
Here are 28 public repositories matching this topic...
Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.
ml pytorch computational-chemistry drug-discovery docking rdkit drug-design geometric-deep-learning molecular-docking protein-ligand gnina alphafold3 flowmatching posebusters
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May 14, 2026 - Python
drugdesign.org source of truth
bioinformatics cheminformatics molecular-dynamics drug-discovery drugs drug-design qsar molecular-modeling molecular-similarity molecular-docking library-design protein-ligand database-searching structure-activity-relationships
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Feb 18, 2024
Target-aware Variational Auto-encoders for Ligand Generation with Multimodal Protein Representation Learning
variational-autoencoder geometric-deep-learning multimodal-deep-learning graph-neural-networks protein-ligand generative-ai
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May 17, 2024 - Python
Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2021)
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Jul 12, 2025 - Jupyter Notebook
A Python tool for automated identification and topological analysis (QTAIM) of Critical Points at the interface between molecular fragments.
python dft vmd computational-chemistry critical-points qtaim non-covalent-interactions multiwfn topological-analysis protein-ligand molecular-interactions bond-critical-points
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Mar 25, 2026 - Python
Identifies relevant ligands in the PDB
python bioinformatics cheminformatics structural-biology pdb drug-discovery mmcif ligands protein-ligand
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Jul 28, 2026 - Python
Open-sourced docking for small molecule to protein target. It prioritizes enhanced user-friendliness and accessibility.
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Jun 3, 2026 - Jupyter Notebook
High-throughput docking pose validation: symmetry-corrected RMSD and lightweight PoseBusters-style distance/clash filters.
cheminformatics pytorch drug-discovery rdkit rmsd molecular-docking protein-ligand posebusters pose-validation symmetry-correction
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Feb 19, 2026 - Python
Public repository of the PDBe ligand environment component
visualization bioinformatics typescript structural-biology pdb drug-discovery protein-ligand molecular-interactions ligand-interactions
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Aug 5, 2026 - TypeScript
Template-based protein-ligand pose prediction with web interface.
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Mar 17, 2026 - Python
R shiny app to analyse microscale thermophoresis (MST) data
data-analysis protein-ligand-interactions protein-ligand-binding-affinity protein-ligand microscale-thermophoresis
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Feb 3, 2026 - R
Two R shiny apps developed for analyzing differential scanning fluorimetry (DSF) data. One for binding, and one for stability
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Aug 12, 2026 - R
A collection of GROMACS molecular dynamics simulation projects featuring protein-only and protein–ligand systems using CHARMM36, AMBER99SB, and physiological ionic conditions.
linux bioinformatics molecular-dynamics computational-biology molecular-simulation drug-discovery gromacs protein-ligand-interactions protein-ligand charmm36 amber99sb
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Jul 31, 2026 - Rich Text Format
Agent skill for routing small-molecule design tasks to open tools, focused references, and license-aware implementation paths.
bioinformatics cheminformatics computational-biology open-science drug-discovery workflow-automation qsar ai-agents molecular-modeling molecular-docking research-software admet retrosynthesis molecular-generation small-molecules medicinal-chemistry protein-ligand agentic-ai agent-skills biological-research
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Jun 30, 2026 - Python
A modern web port of VHELIBS, the Validation Helper for LIgands and Binding Sites: analyse PDB/UniProt structures for RSR, RSCC, occupancy and R-free quality, browse results with interactive filters, and inspect ligands and their electron density in an in-browser Mol* 3D viewer.
flask bioinformatics cheminformatics structural-biology pdb crystallography x-ray-crystallography protein-ligand molstar
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Jul 24, 2026 - Python
Performs large-scale ligand identification, curation and extraction from structures in the Protein Data Bank.
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Jul 31, 2026 - Python
Fine-tuning OpenFold3 (4.0.0) for PDE10A protein–ligand pose prediction via distribution-aware PDB-scale data augmentation: +0.20 PL LDDT, −2.3 Å ligand RMSD on held-out.
bioinformatics cheminformatics structural-biology pdb protein-structure drug-discovery umap domain-adaptation fine-tuning pose-prediction protein-ligand esm2 openfold3 co-folding pde10a morgan-fingerprint butina-clustering
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Jun 4, 2026 - Python
E(3)-equivariant GNNs for protein-ligand binding-affinity prediction (EGNN + e3nn tensor-product), with a machine-precision invariance test suite.
bioinformatics deep-learning cheminformatics structural-biology protein-structure computational-biology pytorch drug-discovery message-passing geometric-deep-learning graph-neural-networks pytorch-geometric binding-affinity protein-ligand egnn e3nn equivariant-neural-networks se3-equivariance molecular-machine-learning pdbbind
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Jul 16, 2026 - Python
Real-time, physics-only protein-ligand force viewer in the browser — LJ+Coulomb force heatmap, SMILES to 3D ligands, PDB-by-ID, binding-site scan. No ML, no docking.
webgl threejs cheminformatics structural-biology molecular-graphics computational-chemistry force-field smiles interactive-visualization biophysics vite molecular-visualization protein-ligand
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Jul 1, 2026 - JavaScript
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