alphafold3

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.

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

[JCIM 2026] Biasing Conformational Sampling in AlphaFold 3 and Boltz-2 via Pair Representation Scaling

Multi-target protein binder design for specificity and cross-reactivity.

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

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

Code for OXtal, an all-atom diffusion model for molecular crystal structure prediction.

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.

A drop-in, hardware-agnostic library for Fused Triangle Multiplicative Updates across AlphaFold3-family models, powered by CUTLASS CuTe kernels.

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

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

A Snakemake workflow for high-throughput AlphaFold 3 structure predictions

Calibrated abstention benchmark for drug–target interaction prediction, grounded in physical difficulty coordinates

🧬 Companion repository for the Methods in Molecular Biology protocol 📓 combining AlphaFold confidence metrics with pyDock energy scoring⚡ for protein–protein complex modeling.

Analysis toolkit for AlphaFold3 biomolecular complex predictions (Protein-DNA, Protein-RNA, Protein-Ligand). Parses PAE error matrices, SASA, and interface binding energies.

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

Generate JSON files of Protein Complex for AlphaFold3