Author

D. Akpinaroglu

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· 1 Biophysics· 1 Cell Biology· 1

Signature Assays, Organisms & Methods

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Approach:deep learning· 2 Organism:C. elegans· 1 Research Focus:cell signaling & trafficking· 1 Research Focus:development & morphogenesis· 1 Approach:experimental assay· 1 Assay:imaging· 1 Research Focus:protein design· 1 Assay:protein sequence· 1

Frequent Co-Authors

A. Guo· 1 shared E. Zhu· 1 shared J. A. Ruffolo· 1 shared J. Feldman· 1 shared J. J. Gray· 1 shared J. Lee· 1 shared K. Seki· 1 shared K. Shen· 1 shared

Activity by Year

2021-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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1 shared paperBioengineering

A. Guo

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3 papers

Recent·Most cited

Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space

D. Akpinaroglu, K. Seki, A. Guo, E. Zhu, M. J. Kelly, T. Kortemme

This paper introduces Frame2seq, a structure-conditioned masked language model for protein sequence design that generates novel, stable proteins with low sequence identity to native sequences.

bioRxiv · Dec 15, 2023 · PreprintBioengineering

Separable mechanisms drive local and global polarity establishment in the C. elegans intestinal epithelium

M. A. Pickett, M. D. Sallee, V. F. Naturale, D. Akpinaroglu, J. Lee, K. Shen, J. Feldman

The paper shows that local and global polarity in C. elegans intestinal epithelium are temporally and genetically separable, with distinct roles for PAR-3 and PKC-3/aPKC.

bioRxiv · Nov 1, 2021Cell Biology

Improved antibody structure prediction by deep learning of side chain conformations

D. Akpinaroglu, J. A. Ruffolo, S. P. Mahajan, J. J. Gray

This paper introduces DeepSCAb, a deep learning method that improves antibody structure prediction by modeling side chain conformations, outperforming existing methods that lack side chain context.

bioRxiv · Sep 22, 2021Biophysics