Local Interaction Score (LIS) for structure prediction analysis

Democratizing AlphaFold3: an PyTorch reimplementation to accelerate protein structure prediction

Step-by-step guide to install and configure AlphaFold 3 using a Conda Python 3.11 environment. No system-wide installations required. ✅ Miniconda setup & dependencies ✅ Repository cloning & model setup ✅ Database configuration & execution script 🔹 Requirements: Linux, NVIDIA GPU (Ampere+), CUDA, ~700GB disk space.

This repository contains the AlphaCutter.py for the removal of non-globular regions from predicted protein structures.

Nextflow, WDL and other bioinformatics pipelines for testing our pipeline monitoring platform

Nextflow, WDL, and HPC pipeline monitoring and optimization running on AWS EC2 ☁️

Ready-to-go Jupyter notebook for plotting AlphaFold-generated MSAs, per-residue pLDDT, and PAE.

A Snakemake workflow for high-throughput AlphaFold 3 structure predictions

fold2go is a nextflow pipeline for in silico prediction of protein structures and interactions through various machine learning models.

🧬 Integrates AlphaFold2/3 model confidence with ⚡ pyDock energy scoring to enhance protein–protein complex prediction accuracy. 📦 Includes workflows for generating diverse AF2-Multimer models, 🔍 computing pyDock energies, and 🔗 combining both via z-score normalization to produce robust, prioritized complex structures.

A collection of helpful Python3 Jupyter notebooks for working with AF3. My first repository so please be nice :)

Generate JSON files of Protein Complex for AlphaFold3

Run AlphaFold 3 protein structure prediction natively on Apple Silicon Macs (M1/M2/M3/M4). MLX inference, web UI, restraint-guided docking.

🧪Predicting 🧬RNA 3D Structures 🚀ML

AlphaFold3 GUI for easy creating covalent bonds, generating entities and exporting to JSON.

AlphaFold 3 inference pipeline — structure prediction for proteins, DNA, RNA, and small molecules. Includes pLDDT/pAE confidence visualisation, CIF output parsing, and py3Dmol 3D structure rendering.

easyFold is an interactive, structure-aware platform for AlphaFold3 job management, visualization, and domain-level interpretation. It integrates confidence metrics (pLDDT, PAE), contact maps, and automated domain segmentation to enable deep, interpretable analysis of predicted protein structures.

a score inference server using protein folding models and FastAPI

Bioinformatics Course - Protein Module Practice

KMer level tokenizer for DNA & Proteins sequences