It is determined that portions of protein sequence space, despite being unobserved in nature, contains many functional proteins that cannot be predicted accurately in silico, providing experimental support for the hypothesis that natural protein sequences explored by evolution represent a miniscule fraction of all possible functional sequences.
This work decomposes canonical proteins, intergenic sequences, and recently emerged yeast and fly de novo proteins, together with randomized controls, into short, interpretable fragments (k-mers) and compares them using alignment-free distances.
Lars A. Eicholt, Á. Tóth-Petróczy, R. Goldstein et al.· bioRxiv· 1 citation
Multiple sequence alignment (MSA) Pairformer is presented, a protein language model that builds on AlphaFold2/3's bidirectional refinement between sequence and pairwise residue representations to accurately model the evolution of protein-protein interactions, despite training exclusively on individual chains.
Yo Akiyama, Zhidian Zhang, Olivia Tang et al.· Cell· 3 citations
Applications to thioredoxins, visual opsins, and Tara Oceans environmental diatom cold-shock proteins show that PLMView can move from interpretable residue-level determinants in well-studied protein families to large-scale environmental functional discovery, linking molecular specialization to ecological distribution a...
The discordance persists: pLDDT correlates positively with PUNCH2 disorder in random and de novo proteins and negatively with β-strand fraction, opposite to the conserved and disordered baselines, a concrete failure mode that protein designers and other working on sequences remote in sequence space should be aware of w...
Lars A. Eicholt, Lasse Middendorf· bioRxiv· 0 citations
Whether AlphaFold 3 complex prediction, combined with STRING evidence and domain-level analysis of interfaces and interaction partners, can help identify and characterize DUF-containing proteins and suggest roles for DUF4130 in nucleic-acid-associated radical-SAM biology and DUF5819 in a bacterial system related to vit...
Lino Riepenhausen, Francesco Costa, Antonina Andreeva et al.· bioRxiv· 0 citations
It is found that many GigaRef singletons belong to a cluster under alternative parameter settings, suggesting that genomic and metagenomic datasets may require dataset-specific clustering configurations, and it is shown that singletons share mutual information with clustered sequences, making them learnable by PLMs and...
R. Vinod, Samir Char, Ava A. Amini et al.· bioRxiv· 0 citations
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