BIORXIVbioRxivbioRxivCold Spring Harbor Laboratory10.1101/2025.10.21.6833501Regular Articlenew resultsbiochemistryDecoding the physicochemical basis of taxonomy preferences in protein design modelsUniProthttp://www.uniprot.org/RRID:SCR_002380Software and Algorithmspython-bxhttps://github.com/bxlab/bx-pythonRRID:SCR_024202Software and AlgorithmsCD-HIThttp://weizhong-lab.ucsd.edu/cd-hit/RRID:SCR_007105Software and AlgorithmsBiopythonhttp://biopython.orgRRID:SCR_007173Software and AlgorithmsNumPyhttp://www.numpy.orgRRID:SCR_008633Software and Algorithms