Open-source alternatives to Openfold

Official implementation for Scaffold-Lab: Critical Evaluation and Ranking of Protein Backbone Generation Methods in A Unified Framework.

This repository is for the paper submitted to the 2021 NeurIPS Benchmark track.

SidechainNet

The preprint can be found here: https://doi.org/10.64898/2025.12.09.693122

Dayhoff is an Atlas of both protein sequence data and generative language models — a centralized resource that brings together 3.34 billion protein sequences across 1.7 billion clusters of metagenomic and natural protein sequences (GigaRef), 46 million structure-based synthetic sequences…

This is the code for AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for optimizing antibody binding affinity. We use experimental antibody–antigen binding affinity measurements to evaluate the performance of widely used computational models for antibody sequence engineering,…

Overview - Results - Resources - How to contribute? - Usage and reproducibility - Acknowledgements - Releases - License - Reference - Links

PDFBench is the first comprehensive benchmark for function-guided de novo protein design.

This is the official code repository for the paper FLOP: Tasks for Fitness Landscapes Of Protein wildtypes by Groth et al. (2023, preprint at https://www.biorxiv.org/content/10.1101/2023.06.21.545880v1), which is currently under review.

DomainBed is a PyTorch suite containing benchmark datasets and algorithms for domain generalization, as introduced in In Search of Lost Domain Generalization.

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This is a companion repository to the paper:

Source code of the paper "PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design"

Code supporting the Protein Design Archive (PDA) database publication

PDBench is a dataset and software package for evaluating fixed-backbone sequence design algorithms. The structures included in PDBench have been chosen to account for the diversity and quality of observed protein structures, giving a more holistic view of performance.