Lightweight Python utility for calculating Solvent Accessible Surface Area (SASA) and pLDDT confidence metrics for AlphaFold2 protein binding pockets.
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Aug 8, 2026 - Python
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plddt
Here are 5 public repositories matching this topic...
Headless molecular visualization and structural biophysics skill for AI agents. Generates publication renders, AlphaFold pLDDT maps, binding pockets, alignments, and web dashboards via PyMOL and OSMesa.
python bioinformatics structural-biology pdb protein-structure computational-biology pymol osmesa superposition mmcif biophysics structural-bioinformatics 3dmol molecular-visualization headless-rendering alphafold macromolecules binding-pocket agent-skill plddt
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Sep 18, 2026 - HTML
Agent skill and pipeline to retrieve, analyze, and visualize AlphaFold predicted structures with interactive 3D WebGL, pLDDT metrics, and PAE domain heatmaps in Canvas.
python webgl bioinformatics structural-biology protein-structure computational-biology gemini uniprot ai-agents protein-folding molecular-visualization alphafold canvas-ui agent-skill 3dmoljs intrinsic-disorder plddt alphafold-database predicted-aligned-error domain-boundary-detection
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Aug 25, 2026 - Python
A measured benchmark of structure prediction confidence, reporting pLDDT calibration against lDDT, the physical validity of predicted structures, and what docking into a predicted receptor costs against docking into the crystal structure it was built from.
python bash benchmark structural-biology computational-biology reproducibility pae structural-bioinformatics protein-structure-prediction molecular-docking coronavirus confidence-calibration boltz alphafold2 colabfold spike-protein pedv plddt lddt openstructure
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Sep 28, 2026 - Python
AlphaFold and PDB confidence and geometry quality gate. Fixed the clash detector flagging every normal peptide bond as a false steric clash on real full-atom structures (the demo's CA-only fixture never exposed it).
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Aug 5, 2026 - Python
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