Author

Qiyao Zhu

Flatiron InstituteORCID 0000-0002-9184-0683Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Approach:statistical model· 2 Approach:deep learning· 1 Research Focus:protein design· 1 Assay:protein sequence· 1 Research Focus:software / tool· 1

Frequent Co-Authors

Vikram Khipple MulliganiD· 2 shared Dennis E. ShashaiD· 1 shared Noora AzadvariiD· 1 shared P. Douglas RenfrewiD· 1 shared Parisa HosseinzadehiD· 1 shared SM Bargeen Alam TurzoiD· 1 shared Tristan ZaborniakiD· 1 shared

Activity by Year

2025-2025 · peak 2/yr

Co-Author Collaboration Network

7 top collaborators · 16 mutual co-author links

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2 shared papersMolecular Biology

Vikram Khipple MulliganORCID

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2 papers

Recent·Most cited

Heuristic energy-based cyclic peptide design

Qiyao Zhu, Vikram Khipple Mulligan, Dennis E. Shasha

This paper introduces CyclicChamp, a computational pipeline for designing cyclic peptides of 7-24 residues, achieving stable designs validated by molecular dynamics simulations.

PLoS Computational Biology · Apr 30, 2025Peer-reviewedMolecular Biology

The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design

Tristan Zaborniak, Noora Azadvari, Qiyao Zhu, SM Bargeen Alam Turzo, Parisa Hosseinzadeh, P. Douglas Renfrew, Vikram Khipple Mulligan

The paper introduces Masala, an open-source software suite designed to extend and improve upon Rosetta for synthetic heteropolymer design, offering modular architecture and performance improvements.

Methods in enzymology on CD-ROM/Methods in enzymology · Jan 1, 2025Peer-reviewedBiochemistry