References

DeepFRI is described in:

Gligorijevic V, et al. 2021. Structure-based protein function prediction using graph convolutional networks. Nature Communications, 12, 3168.

DeepFRI is dependent on:

Software

Reference

TensorFlow

Abadi M, et al. 2015. TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems. ArXiv

Scikit-Learn

Pedregosa F, et al. 2011. Scikit-learn: Machine Learning in Python. Journal of Machine Learning Research, 12, 2825-2830.

Biopython

Cock PJA, et al. 2009. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 11, 1422-1423.

DeepFRI was used in:

Maranga M, et al. 2022. Comprehensive function annotation of metagenomes and microbial genomes using a deep learning-based method. mSystems, 2023.

Metagenomic-DeepFRI is dependent on:

Software

Reference

MMseqs2

Steinegger M and Söding J 2017. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 35, 1026-1028.

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