Author

A. Khmelinskaia

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· 3 Biochemistry· 1 Biophysics· 1 Scientific Communication & Education· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 4 Approach:deep learning· 3 Assay:protein structure· 3 Approach:statistical model· 3 Research Focus:drug response / drug discovery· 2 Research Focus:protein folding & dynamics· 2 Research Focus:cell signaling & trafficking· 1 Research Focus:cell type annotation· 1

Frequent Co-Authors

D. Baker· 5 shared N. P. King· 5 shared A. J. Borst· 3 shared E. C. Yang· 3 shared S. Chan· 3 shared W. Sheffler· 3 shared A. Antanasijevic· 2 shared J. Y. Wang· 2 shared

Activity by Year

2021-2023 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 43 mutual co-author links

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5 shared papersBioengineering

D. Baker

Mutual co-authors in cluster

Author profile →

6 papers

Recent·Most cited

Local structural flexibility drives oligomorphism in computationally designed protein assemblies

A. Khmelinskaia, N. P. Bethel, F. Fatehi, A. Antanasijevic, A. J. Borst, S.-H. Lai, J. Y. Wang, B. Basu Mallik, M. M. Miranda, A. M. Watkins, C. Ogohara, S. Caldwell, M. Wu, A. J. R. Heck, D. Veesler, , N. P. King

This study shows that structural flexibility in computationally designed protein assemblies leads to multiple architectures, expanding their functional possibilities.

bioRxiv · Oct 18, 2023Bioengineering

Computational design of non-porous, pH-responsive antibody nanoparticles

E. C. Yang, R. Divine, M. C. Miranda, A. J. Borst, W. Sheffler, J. Z. Zhang, J. Decarreau, A. Sarajovi, M. Abedi, N. Goldbach, M. Ahlrichs, C. Dobbins, A. Hand, S. Cheng, M. Lamb, , D. Baker

This paper designs pH-responsive antibody nanoparticles with three distinct protein components that disassemble at tunable pH levels, enabling targeted delivery of biologics.

bioRxiv · Apr 17, 2023Bioengineering

Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock

W. Sheffler, E. C. Yang, Q. Dowling, Y. Hsia, C. N. Fries, J. Stanislaw, M. Langowski, M. Brandys, A. Khmelinskaia, N. P. King, D. Baker

RPXDock enables fast, flexible protein docking for symmetric architectures, supporting diverse applications in nanomaterial design.

bioRxiv · Oct 25, 2022Bioengineering

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains

J. Y. Wang, A. Khmelinskaia, W. Sheffler, M. C. Miranda, A. Antanasijevic, A. J. Borst, S. V. Torres, C. Shu, Y. Hsia, U. Nattermann, D. Ellis, C. Walkey, M. Ahlrichs, S. Chan, A. Kang, , N. P. King

This study identifies cryptic transmembrane domains in designed protein nanoparticles that hinder secretion and introduces a computational tool, Degreaser, to remove them while maintaining stability, improving secretion efficiency.

bioRxiv · Aug 4, 2022Biochemistry

Increasing computational protein design literacy through cohort-based learning for undergraduate students

E. C. Yang, R. Divine, C. S. Kang, S. Chan, E. Arenas, Z. Subol, P. Tinker, H. Manninen, A. Feichtenbiner, T. Mustafa, J. Hallowell, I. Orr, H. Haddox, B. Koepnick, J. O'Connor, , N. P. King

This paper describes a remote cohort-based curriculum for undergraduate students to learn computational protein design, enhancing their research skills and connecting them with the lab.

bioRxiv · May 24, 2022Scientific Communication & Education

ATP driven diffusiophoresis: active cargo transport without motor proteins

B. Ramm, A. Goychuk, A. Khmelinskaia, P. Blumhardt, K. A. Ganzinger, E. Frey, P. Schwille

The paper demonstrates a non-specific physical mechanism for active cargo transport using the MinDE protein system in E. coli, sorting cargo by size through diffusiophoresis.

Nature Physics · Apr 5, 2021Peer-reviewedBiophysics