Key Resources Table

Reagent or Resource	Source	Identifier
Deposited Data
Protein sequence data	Szklarczyk et al., 2019	https://string-db.org/
Protein interaction data	Szklarczyk et al., 2019	https://string-db.org/
Docking benchmark dataset	Hwang et al., 2010	https://zlab.umassmed.edu/benchmark/
SARS-CoV-2 sequences and interactions	Gordon et al., 2020	https://www.ebi.ac.uk/pride/archive/projects/PXD018117
ARS-UCD1.2 Bos taurus genome assembly	NCBI Assembly	https://www.ncbi.nlm.nih.gov/assembly/GCF_002263795.1/
GSE160028 Bos taurus RNA-seq	Halstead et al. 2021	https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE160028
Processed data, trained models, and new predictions	This study	https://doi.org/10.5281/zenodo.5140612
Software and Algorithms
D-SCRIPT	This study	http://dscript.csail.mit.edu/(https://doi.org/10.5281/zenodo.5140508)
Protein sequence embeddings	Bepler & Berger 2019	https://github.com/tbepler/protein-sequence-embedding-iclr2019
PIPR	Chen et al., 2019	https://github.com/muhaochen/seq_ppi
DeepPPI	Richoux et al., 2019	https://gitlab.univ-nantes.fr/richoux-f/DeepPPI
DSD	Cao et al. 2014	https://dsd.cs.tufts.edu/capdsd
CD-HIT	Fu et al., 2012	http://weizhongli-lab.org/cd-hit/
GOGO	Zhao et al., 2018	http://dna.cs.miami.edu/GOGO/
POT Python Optimal Transport	Flamary et al., 2017	https://pythonot.github.io/