Design of high-affinity binders to immune modulating receptors for cancer immunotherapy

Authors: Wei Yang, Derrick R. Hicks, Agnidipta Ghosh, Tristin A. Schwartze, Brian Conventry, Inna Goreshnik, Aza Allen, Samer F. Halabiya, Chan Johng Kim, Cynthia S. Hinck, David S. Lee, Asim K. Bera, Zhe Li, Yujia Wang, Thomas Schlichthaerle, Longxing Cao, Buwei Huang, Sarah Garrett, Stacey R. Gerben, Stephen Rettie, Piper Heine, Analisa Murray, Natasha Edman, Lauren Carter, Lance Stewart, Steven C. Almo, Andrew P. Hinck, David Baker

Source: Nature Communications, Vol 16, Iss 1, Pp 1-12 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f483d8972b2f4000b76c750e2fb8c6fc

Directing polymorph specific calcium carbonate formation with de novo protein templates

Authors: Fatima A. Davila-Hernandez, Biao Jin, Harley Pyles, Shuai Zhang, Zheming Wang, Timothy F. Huddy, Asim K. Bera, Alex Kang, Chun-Long Chen, James J. De Yoreo, David Baker

Source: Nature Communications, Vol 14, Iss 1, Pp 1-11 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/6cacd6f254a84ca6bc2400ddc3231925

De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8

Authors: Anindya Roy, Lei Shi, Ashley Chang, Xianchi Dong, Andres Fernandez, John C. Kraft, Jing Li, Viet Q. Le, Rebecca Viazzo Winegar, Gerald Maxwell Cherf, Dean Slocum, P. Daniel Poulson, Garrett E. Casper, Mary L. Vallecillo-Zúniga, Jonard Corpuz Valdoz, Marcos C. Miranda, Hua Bai, Yakov Kipnis, Audrey Olshefsky, Tanu Priya, Lauren Carter, Rashmi Ravichandran, Cameron M. Chow, Max R. Johnson, Suna Cheng, McKaela Smith, Catherine Overed-Sayer, Donna K. Finch, David Lowe, Asim K. Bera, Gustavo Matute-Bello, Timothy P. Birkland, Frank DiMaio, Ganesh Raghu, Jennifer R. Cochran, Lance J. Stewart, Melody G. Campbell, Pam M. Van Ry, Timothy Springer, David Baker

Source: Nature Communications, Vol 14, Iss 1, Pp 1-18 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/e3c311aafe5446188603fdc35eee2511

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites

Authors: Parisa Hosseinzadeh, Paris R. Watson, Timothy W. Craven, Xinting Li, Stephen Rettie, Fátima Pardo-Avila, Asim K. Bera, Vikram Khipple Mulligan, Peilong Lu, Alexander S. Ford, Brian D. Weitzner, Lance J. Stewart, Adam P. Moyer, Maddalena Di Piazza, Joshua G. Whalen, Per Jr. Greisen, David W. Christianson, David Baker

Source: Nature Communications, Vol 12, Iss 1, Pp 1-12 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/603d7c9cce674f14a81d38644247320d

Design of multi-scale protein complexes by hierarchical building block fusion

Authors: Yang Hsia, Rubul Mout, William Sheffler, Natasha I. Edman, Ivan Vulovic, Young-Jun Park, Rachel L. Redler, Matthew J. Bick, Asim K. Bera, Alexis Courbet, Alex Kang, T. J. Brunette, Una Nattermann, Evelyn Tsai, Ayesha Saleem, Cameron M. Chow, Damian Ekiert, Gira Bhabha, David Veesler, David Baker

Source: Nature Communications, Vol 12, Iss 1, Pp 1-10 (2021)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/8bb80e33cedb4e58856a97a798a217fd

Large-scale design and refinement of stable proteins using sequence-only models

Authors: Jedediah M. Singer, Scott Novotney, Devin Strickland, Hugh K. Haddox, Nicholas Leiby, Gabriel J. Rocklin, Cameron M. Chow, Anindya Roy, Asim K. Bera, Francis C. Motta, Longxing Cao, Eva-Maria Strauch, Tamuka M. Chidyausiku, Alex Ford, Ethan Ho, Alexander Zaitzeff, Craig O. Mackenzie, Hamed Eramian, Frank DiMaio, Gevorg Grigoryan, Matthew Vaughn, Lance J. Stewart, David Baker, Eric Klavins

Source: PLoS ONE, Vol 17, Iss 3 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8920274/?tool=EBI; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/6bc977c80731465da8bb65f2719bfb0c

Structure and Characterization of a Covalent Inhibitor of Src Kinase

Authors: Deepak Gurbani, Guangyan Du, Nathaniel J. Henning, Suman Rao, Asim K. Bera, Tinghu Zhang, Nathanael S. Gray, Kenneth D. Westover

Source: Frontiers in Molecular Biosciences, Vol 7 (2020)

Subject Terms: src kinase, cancer, dasatinib, selectivity, irreversible inhibitor, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmolb.2020.00081/full; https://doaj.org/toc/2296-889X

Access URL: https://doaj.org/article/2ccc48f356d64ae1837bcf1a0936c482

Large-scale design and refinement of stable proteins using sequence-only models.

Authors: Jedediah M Singer, Scott Novotney, Devin Strickland, Hugh K Haddox, Nicholas Leiby, Gabriel J Rocklin, Cameron M Chow, Anindya Roy, Asim K Bera, Francis C Motta, Longxing Cao, Eva-Maria Strauch, Tamuka M Chidyausiku, Alex Ford, Ethan Ho, Alexander Zaitzeff, Craig O Mackenzie, Hamed Eramian, Frank DiMaio, Gevorg Grigoryan, Matthew Vaughn, Lance J Stewart, David Baker, Eric Klavins

Source: PLoS ONE, Vol 17, Iss 3, p e0265020 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/7aded064f9274cf1893c7889f59dfe6b

The nonreceptor tyrosine kinase SRMS inhibits autophagy and promotes tumor growth by phosphorylating the scaffolding protein FKBP51.

Authors: Jung Mi Park, Seung Wook Yang, Wei Zhuang, Asim K Bera, Yan Liu, Deepak Gurbani, Sergei J von Hoyningen-Huene, Sadie Miki Sakurada, Haiyun Gan, Shondra M Pruett-Miller, Kenneth D Westover, Malia B Potts

Source: PLoS Biology, Vol 19, Iss 6, p e3001281 (2021)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1544-9173; https://doaj.org/toc/1545-7885

Access URL: https://doaj.org/article/4164afef6c64473eae9b0a547aaea3fd

Crystal structures of Moorella thermoacetica cyanuric acid hydrolase reveal conformational flexibility and asymmetry important for catalysis.

Authors: Ke Shi, Seunghee Cho, Kelly G Aukema, Thomas Lee, Asim K Bera, Jennifer L Seffernick, Lawrence P Wackett, Hideki Aihara

Source: PLoS ONE, Vol 14, Iss 6, p e0216979 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/d94a26c1a447421fb9bd64f203e32a83