Author

Mark Fingerhuth

ProteinQure (Canada)ORCID 0000-0002-0867-4697Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Assay:proteomics· 2 Research Focus:drug response / drug discovery· 1 Research Focus:protein design· 1

Frequent Co-Authors

Alexander KitaygorodskyiD· 2 shared Aron BroomiD· 2 shared Ashlin K KanawatyiD· 2 shared Elliot LayneiD· 2 shared Glenn L. ButterfossiD· 2 shared Anita K. NivedhaiD· 1 shared Caroline WoffindaleiD· 1 shared David Earl HostalleroiD· 1 shared

Activity by Year

2025-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 41 mutual co-author links

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2 shared papersBioengineering

Alexander KitaygorodskyORCID

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2 papers

Recent·Most cited

AtomWeaver: Multi-Component Flow Matching with a Structured Geometric Prior Facilitates Non-Canonical Peptide Design

Alexander Kitaygorodsky, David Earl Hostallero, Aron Broom, Elliot Layne, Sungwon Hwang, Ashlin K Kanawaty, Tomáš Babej, Glenn L. Butterfoss, Mark Fingerhuth

AtomWeaver enables non-canonical peptide design by using a geometric prior to generate side-chain atoms without restricting residue identity, achieving high agreement with experimental results.

bioRxiv · Sep 28, 2026 · PreprintBioengineering

Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding

Elliot Layne, Ashlin K Kanawaty, Aron Broom, Alexander Kitaygorodsky, Anita K. Nivedha, Parth Vora, Caroline Woffindale, Sarah Hailstone, Eirini Sachouli, Ella Halcrow, Gillian E. Donachie, Michelle Adsett, Glenn L. Butterfoss, Mark Fingerhuth

This paper improves de novo peptide binder design by combining peptide-specific finetuning with a novel decoding order strategy, achieving a 16-30% increase in in silico success rates and doubling top-ranking agonists for OPRM1.

bioRxiv · Oct 28, 2025 · PreprintBioengineering