Author

J. Nivala

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioengineering· 2 Biophysics· 2

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Research Focus:protein folding & dynamics· 2 Assay:protein structure· 2 Assay:DNA methylation· 1 Organism:human· 1 Research Focus:protein design· 1

Frequent Co-Authors

D. Baker· 2 shared D. Juergens· 2 shared M. Lamb· 2 shared P. J. Y. Leung· 2 shared P. M. Levine· 2 shared X. Li· 2 shared A. Broerman· 1 shared A. F. Dishman· 1 shared

Activity by Year

2021-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 42 mutual co-author links

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2 shared papersBiophysics

D. Baker

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Author profile →

4 papers

Recent·Most cited

Multi-pass, single-molecule nanopore reading of long protein strands with single-amino acid sensitivity

K. Motone, D. Kontogiorgos-Heintz, J. Wee, K. Kurihara, S. Yang, G. Roote, Y. Fang, N. Cardozo, J. Nivala

This paper demonstrates a method to sequence long protein strands with single-amino-acid sensitivity using nanopore sensors and ClpX unfoldase, enabling accurate protein barcode sequencing and analysis of folded protein domains.

bioRxiv · Oct 19, 2023 · PreprintBiophysics

Design of stimulus-responsive two-state hinge proteins

F. Praetorius, P. J. Y. Leung, M. H. Tessmer, A. Broerman, C. Demakis, A. F. Dishman, A. Pillai, A. Idris, D. Juergens, J. Dauparas, X. Li, P. M. Levine, M. Lamb, R. K. Ballard, S. R. Gerben, , D. Baker

This paper designs two-state hinge proteins that switch between structural states in response to ligands, demonstrating atomic-level accuracy and tunable kinetics and thermodynamics.

bioRxiv · Jan 27, 2023Biophysics

De novo design of high-affinity protein binders to bioactive helical peptides

S. Vazquez Torres, P. J. Y. Leung, I. D. Lutz, P. Venkatesh, J. L. Watson, F. Hink, H.-H. Huynh, A. H.-W. Yeh, D. Juergens, N. R. Bennett, A. N. Hoofnagle, E. Huang, M. J. MacCoss, M. Exposit, G. R. Lee, , D. Baker

This paper designs high-affinity protein binders for bioactive helical peptides using deep learning and generative models, achieving picomolar affinity without experimental optimization.

bioRxiv · Dec 10, 2022 · PreprintBioengineering

A nanopore interface for high bandwidth DNA computing

K. Zhang, Y.-J. Chen, K. Doroschak, K. Strauss, L. Ceze, G. Seelig, J. Nivala

This paper introduces a nanopore-based readout method for DNA strand displacement circuits, achieving higher output bandwidth than fluorescence spectroscopy for molecular diagnostics.

bioRxiv · Dec 30, 2021 · PreprintBioengineering