chimerax 开源项目推荐（34 个）

rdk /p2rank

P2Rank: Protein-ligand binding site prediction from protein structure based on machine learning.

jvogan /proteus

Structural biology superpowers for AI coding agents: PyMOL, ChimeraX, AlphaFold DB, RCSB PDB, UniProt, and Rosetta workflows.

ScheltemaLab /ChimeraX_XMAS_bundle

该项目在 GitHub 上没有填写描述

wtaisner /chimerax-ligand-recognizer

This bundle provides ChimeraX command for recognizing ligands in cryoEM and X-ray crystallography maps using deep learning.

sami-chaaban /PointPAE

Map AlphaFold PAE values on a model

ajs99778 /ChimeraX_OpenCommands

run commands when opening files

piercetaylor /af3-to-amber-md-sim

Takes an AlphaFold3 protein–DNA model through ChimeraX cleanup, tleap topology building, and a staged equilibration and production MD run on a Slurm cluster, for a wild-type and a mutant system in parallel.

danilkotelnikov /Molecullage

Figures of protein structures, sequences, contact maps, pipelines and plots for papers: an HTML page kit printed to vector PDF and PNG, flat ChimeraX renders, QA checks, and a Claude Code skill, hooks and MCP server.

JMB-Scripts /MolNympheas

Pymol & ChimeraX Scripts for color

LUKASinScience /AlphaFold-Guide

A practical, beginner-to-expert guide to AlphaFold2, ColabFold, AlphaFold3, AlphaMissense and ChopChopMF — built while learning to predict and analyze protein structures myself.

mtariqi /struct-kinase-tnbc

Integrative structural bioinformatics and molecular-dynamics analysis of EGFR and PTK2/FAK inhibitor response in triple-negative breast cancer.

maduprey /chimerax-docker

Docker image for the molecular visualization program, UCSF ChimeraX

LUKASinScience /ChopChopMF

Faster, Friendlier Protein Analysis in ChimeraX for everyone

tiffanyhuff /ChimeraXApp

An API to interactively run the UCSF ChimeraX molecular visualization software on the Lonestar6 supercomputer.

JMB-Scripts /PyMeraX

PyMOL tuning to soften molecular rendering

Dhritirajkalitacolab /nigellidine-ftsz-computational-drug-discovery

Three Nigella sativa alkaloids (indazoles nigellidine, nigellicine; isoquinoline nigellimine) vs S. aureus FtsZ (PDB 3VOA): ADMET screening; docking with Vina, AutoDock4, GNINA, DiffDock-L (redock RMSD 0.307 Å); 4I55 tubulin counter-screen; 100 ns MD; MM-GBSA −13.28 ± 0.97 kcal/mol (SD). Computational predictions only.

vib-training-conferences /protein-structure-analysis

该项目在 GitHub 上没有填写描述

maxieds /public-file-stashes

Datasets available FREELY on the PUBLIC Internet. (punctuation)

JMB-Scripts /ConServation-to-PDB

CS-to-PDB is an integrated toolkit for calculating sequence conservation, mapping it onto protein structures, and generating publication-ready structural and sequence visualizations.

GiatrasKon /Algorithms-in-Structural-Bioinformatics-Assignments

Assignments from the 'Algorithms in Structural Bioinformatics' graduate course, exploring RNA folding, molecular conformational analysis, and protein structure comparison using Python and bioinformatics tools.