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Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.
10 papers
Recent·Most cited
C. Liu, K. Wu, H. Choi, H. Han, X. Zhang, J. L. Watson, S. Shijo, A. K. Bera, A. Kang, E. Brackenbrough, B. Coventry, D. R. Hick, A. N. Hoofnagle, P. Zhu, X. Li, , D. Baker
The paper develops RFdiffusion to generate protein binders for IDPs/IDRs, achieving nanomolar affinity and functional applications in amylin and IL2RG.
Nature · Jul 30, 2025Peer-reviewedBiochemistry
K. Wu, H. Jiang, D. R. Hicks, C. Liu, E. Muratspahic, T. A. Ramelot, Y. Liu, K. McNally, A. Gaur, B. Coventry, W. Chen, A. K. Bera, A. Kang, S. Gerben, M. Y.-L. Lamb, , Z. Song
The paper designs proteins that bind intrinsically disordered regions with high affinity and specificity across diverse targets.
bioRxiv · Jul 15, 2024Biochemistry
D. Baker, W. Yang, D. R. Hicks, A. Ghosh, T. A. Schwartze, B. Coventry, I. Goreshnik, A. Allen, S. Halabiya, C. Kim, C. S. Hinck, D. S. Lee, A. Bera, Z. Li, Y. Wang, , A. P. Hinck
This paper designs high-affinity proteins that bind to convex protein sites using geometrically matching concave scaffolds, achieving low nanomolar to picomolar affinities.
bioRxiv · May 1, 2024 · PreprintBiochemistry
C. S. Adams, H. Kim, A. E. Burtner, D. S. Lee, C. Dobbins, C. Criswell, B. Coventry, H. M. Kim, N. P. King
This study designs protein minibinders that act as agonists for TLR3, showing nanomolar binding and biological activity in cell lines.
bioRxiv · Apr 17, 2024Biochemistry
L. An, M. Said, L. Tran, S. Majumder, I. Goreshnik, G. R. Lee, D. Juergens, J. Dauparas, I. Anishchenko, B. Coventry, A. K. Bera, A. Kang, P. M. Levine, V. Alvarez, A. Pillai, , D. Baker
The paper designs nanomolar binders for diverse small molecules using a pseudocycle-based shape complementarity method, enabling direct conversion into sensing systems.
bioRxiv · Dec 20, 2023 · PreprintBiochemistry
G. R. Lee, S. J. Pellock, C. Norn, D. Tischer, J. Dauparas, I. Anishchenko, J. A. M. Mercer, A. Kang, A. Bera, H. Nguyen, I. Goreshnik, D. Vafeados, N. Roullier, H. L. Han, B. Coventry, , D. Baker
This paper designs a protein family that binds and senses small molecules using deep learning and physics-based methods, achieving nanomolar sensitivity for cortisol.
bioRxiv · Nov 1, 2023Biochemistry
T. F. Huddy, Y. Hsia, R. D. Kibler, J. Xu, N. Bethel, D. Nagarajan, R. Redler, P. J. Y. Leung, A. Courbet, E. C. Yang, A. K. Bera, N. Coudray, S. J. Calise, F. A. Davila-Hernandez, C. Weidle, , D. Baker
This paper introduces standardized protein building blocks and geometric design principles to create expandable protein nanomaterials, validated through X-ray crystallography and electron microscopy.
bioRxiv · Jun 9, 2023Biochemistry
N. I. Edman, R. L. Redler, A. Phal, T. Schlichthaerle, S. R. Srivatsan, A. Etemadi, S. An, A. Favor, D. Ehnes, Z. Li, F. Praetorius, M. Gordon, W. Yang, B. Coventry, D. R. Hicks, , D. Baker
This study designs synthetic oligomeric ligands to modulate FGFR signaling and shows their impact on vascular cell fate decisions.
bioRxiv · Mar 14, 2023Bioengineering
N. Bennett, B. Coventry, I. Goreshnik, B. Huang, A. Allen, D. Vafeados, Y. P. Peng, J. Dauparas, M. Baek, L. Stewart, F. DiMaio, S. De Munck, S. Savvides, D. Baker
This paper improves de novo protein binder design by using deep learning models to assess design success rates and computational efficiency.
bioRxiv · Jun 15, 2022Bioengineering
B. L. Trippe, B. Huang, E. A. DeBenedictis, B. Coventry, N. Bhattacharya, K. K. Yang, D. Baker, L. Crawford
The paper introduces randomized sorting in sort-seq assays to eliminate systematic bias, validated through simulation and experiments, and extends the method for variance estimation and multi-bin sorting.
bioRxiv · Feb 17, 2022Bioengineering