Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer). Visit FlyPredictome for large-scale AFM prediction results in fly (now ~800,000 PPIs).
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
Ready-to-go Jupyter notebook for plotting AlphaFold-generated MSAs, per-residue pLDDT, and PAE.
Nextflow, WDL, and HPC pipeline monitoring and optimization running on AWS EC2 ☁️
A Snakemake workflow for high-throughput AlphaFold 3 structure predictions
🧬 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.
fold2go is a nextflow pipeline for in silico prediction of protein structures and interactions through various machine learning models.
A collection of helpful Python3 Jupyter notebooks for working with the AF3 server. My first repository so please be nice :)
Generate JSON files of Protein Complex for AlphaFold3
🧪Predicting 🧬RNA 3D Structures 🚀ML
AlphaFold3 GUI for easy creating covalent bonds, generating entities and exporting to JSON.
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
AI based protein modeling and design
KMer level tokenizer for DNA & Proteins sequences
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