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

Local Interaction Score (LIS) for structure prediction analysis

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

Run AlphaFold2 (and multimer) step by step

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

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

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

Official repository for the OUP published paper: "Computational Design of a Predicted High-Affinity Humanised Nanobody against KRAS Switch-I". Includes the PIA-KRASv2-Nb sequence, 3D models, and validation data.

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

Unified Python library and CLI for protein structure prediction and inverse folding.

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

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).