Joe Hoye Dow ⚡️
Protein structure + AI
AlphaFold3-SeqVisToolkit

AlphaFold3-SeqVisToolkit
AlphaFold3

A lightweight toolkit for visualizing and analyzing AlphaFold3 prediction outputs.
Awesome-IDR-Prediction

Awesome-IDR-Prediction
Protein Disorder Prediction

Curated Labs, Tools for Protein Intrinsic Disorder (IDR) prediction.
Awesome-Protein-ContactMap-Prediction

Awesome-Protein-ContactMap-Prediction
PPI Interface prediction

A curated collection of computational tools for intermolecular interaction prediction, primarily focus on Protein Interface Contact Prediction task.
IDRInter_seq

IDRInter_seq
Transformer

A Transformer model: binary classification task takes two protein sequences (one IDP with IDR and one ordered protein) and their target segment coordinates as inputs, to predict whether physical contact occurs between the fragments at the segment level. The output is a binary label (0/1) or raw logits for interaction probability.
Molecular Dynamic Simulation
Gromacs-Everything-Skill

Gromacs-Everything-Skill
Claude Code skill for Gromacs

Claude Code skill for Gromacs，designed for Molecular Dynamics Simulation Operation & QA.
AmberTools-Everything-Skill

AmberTools-Everything-Skill
Claude Code skill for Amber/AmberTools

Claude code skill for AmberTools，designed for molecular dynamics simulation operation & QA.
gmxplot

gmxplot
Gromacs Visualization

GROMACS XVG File Visualization Tool. Auto-detect, plot, compare, and summarize your GROMACS simulation data from the command line.
PDB-MD-Suite

PDB-MD-Suite
Molecular dynamic workflows

Pre- and post-processing toolkit for PDB/MMCIF structure files in molecular dynamics workflows.
Machine Learning
AI4Bio-LHT

AI4Bio-LHT
LHT template

A clean template to kickstart your deep learning project. Modified to focus on AI4Bio field.

Sklearn-Skill

Sklearn-Skill
Claude Code skill for Scikit-Learn

Claude Code skill for Scikit-Learn，designed for machine learning Coding operation & QA.
Pytorch-Skill

Pytorch-Skill
Claude Code skill for Pytorch

Claude code skill for pytorch code writing.
Pytorch-Template-Skill

Pytorch-Template-Skill
Claude Code skill for pytorch ecosystem

Lightning-Hydra-Template · PyTorch Lightning 2.5.5 · Hydra 1.4 · HuggingFace Ecosystem · Optuna · Visualization & Interpretability. This repository distills the Lightning-Hydra-Template plus the official documentation and example code of the surrounding deep-learning ecosystem into a unified Claude Code Skill — a structured knowledge base covering the full ML engineering stack from project scaffolding to model training, hyperparameter optimization, experiment tracking, and interpretability.
Research tools
pyPaperFlow

pyPaperFlow
Paper reading

An automated literature processing platform for scientific researchers. Batch retrieve, fetch, parse, and structure papers from PubMed, arXiv, bioRxiv, ChemRxiv, and DOI-based sources. From paper retrieval to knowledge internalization, automate the heavy lifting and keep the judgment human.
Repowiki-cli

Repowiki-cli
GitHub coding

Query AI-generated documentation for any public GitHub repository — straight from your terminal. Including three wiki services: DeepWiki · Google Code Wiki · zread.ai.
GhResearcher

GhResearcher
GitHub trending

A powerful GitHub Code & Repo Analysis CLI for Researchers, designed to track activities, scrape and parse repository contexts, and search intelligently—without leaving YOUR terminal.
LibInspector

LibInspector
Python AST analysis

From 'Black Box' to 'Glass Box': A Python library inspection tool. Turn passive code reading into active architectural exploration.
Repo-Inspector

Repo-Inspector
Python repository analysis

Repo-Inspector helps developers and reviewers quickly understand a Python repository. It produces a concise static analysis report and — optionally — deeper runtime inspection output by integrating with LibInspector.
Research Automation
Daily-GitHub-AI4Bio

Daily-GitHub-AI4Bio
GitHub Trending Automation

A template to capture GitHub academic community activity for protein structural AI. It centralizes fragmented research signals, delivering a readable timeline for tracking field developments and discovering emerging trends.
Daily-Paper-Agent-Template

Daily-Paper-Agent-Template
Paper Automation with AI

Biomedical × Computational Interdisciplinary Literature Auto-Tracking + AI Deep Reading Template. Automatically track the latest papers on PubMed · arXiv · bioRxiv · medRxiv · chemRxiv periodically via GitHub Actions, archive the documents and generate weekly Issue reports. An LLM produces a “score + one-sentence summary + abstract translation + 16-section Paper Card + reviewer evaluation” for each paper. A fully searchable GitHub Pages site is deployed, and Zotero is integrated for literature screening and library import.
Daily-Paper-noAgent-Template

Daily-Paper-noAgent-Template
Paper Automation

Automated Literature Alert Template for Biomedical and Computational Interdisciplinary Research. Automatically track the latest papers on PubMed · arXiv · bioRxiv · medRxiv · chemRxiv periodically via GitHub Actions, save duplicates, generate weekly Issue reports, and leverage Zotero and AI tools for screening and intensive reading.