An open-source platform for developing protein models beyond AlphaFold.

Local Interaction Score (LIS) Calculation from AlphaFold-Multimer (Enhanced Protein-Protein Interaction Discovery via AlphaFold-Multimer)

Run AlphaFold2 (and multimer) step by step

RNA, mRNA, DNA, Peptide, Protein, Antibody and Complex | Folding

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

A curated list of awesome protein design research, software and resources.

Code repository for the SPOC tool for scoring binary AF-M predicitons.

Screen interactions with AlphaFold Multimer

GUI for running jobs with a local installation of AlphaFold2. Supports submission to queuing systems.

A Tufts Research Technology Workshop detailing how to use AlphaFold 2 on the Tufts HPC cluster

Map AlphaFold PAE values on a model

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

RAPSAP is a comprehensive archive of protein structures that pertain specifically to autophagy, aimed at improving structural understanding of the biological process

AlphaFold-wrapper for small HPC

Protein-Protein Complex Conformational Sampling via AlphaFold-Multimer and Molecular Dynamics

Computational Design of the PIA-KRASv2-Nb Nanobody: A Humanized KRAS Inhibitor Developed Using the Protein Interaction Architect (PIA) Method, Including 3D Models and Structural Validation.

Repo to build AF models of endogeneous ligands

AlphaFold pulldown implementation adapted from https://github.com/KosinskiLab/AlphaPulldown

AI based protein modeling and design

Here's the code for my master's degree thesis at Università di Pavia (Dipartimento di Biologia e Biotecnologie L. Spallanzani).