P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.
Structural biology superpowers for AI coding agents: PyMOL, ChimeraX, AlphaFold DB, RCSB PDB, UniProt, and Rosetta workflows.
This bundle provides ChimeraX command for recognizing ligands in cryoEM and X-ray crystallography maps using deep learning.
Map AlphaFold PAE values on a model
Pymol & ChimeraX Scripts for color
Integrative structural bioinformatics and molecular-dynamics analysis of EGFR and PTK2/FAK inhibitor response in triple-negative breast cancer.
Docker image for the molecular visualization program, UCSF ChimeraX
PyMOL tuning to soften molecular rendering
An API to interactively run the UCSF ChimeraX molecular visualization software on the Lonestar6 supercomputer.
CS-to-PDB is an integrated toolkit for calculating sequence conservation, mapping it onto protein structures, and generating publication-ready structural and sequence visualizations.
Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.
Interface analysis and publication-ready figures for solved and predicted complexes, from a panel, the command line, or an LLM agent.
π Transform Python code into efficient Rust with p2r, a static transpiler bridging ease of Python with Rust's speed and safety.
Relevant neurological proteins pulled directly from my personal ChimeraX library repo, found on my profile
Porcupine / mode-vector plots (displacement arrows between two protein states) natively in UCSF ChimeraX - no PyMOL required
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