Brian K Shoichet (James S Fraser)

ORCID

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 91

Top Venues

bioRxiv : the preprint server for biology

eLife

Proceedings of the National Academy of Sciences of the United States of America

Science (New York, N.Y.)

University of California San Francisco

University of California Berkeley (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of California San Francisco

United States

Professor :: Bioengineering and Therapeutic Sciences

Education History

University of California Berkeley

United States

PHD :: Molecular and Cell Biology

Publications

Daphne F Chen, Leah Tang Roe, Yuping Li, Adair L Borges, Jenny Y Zhang, Palak Babbar, Sourobh Maji, Maisie G V Stevens, Galen J Correy, Morgan E Diolati, Dominique H Smith, Alan Ashworth, Robert M Stroud, Mark J S Kelly, Joseph Bondy-Denomy, Brian K Shoichet
AcrIF11 is a potent CRISPR-specific ADP-ribosyltransferase encoded by phage and plasmid. bioRxiv : the preprint server for biology (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 12 (2024)
Stephanie A Wankowicz, Brian K Shoichet
Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCrJ 11 (Pt 4) (2024)
Fangyu Liu, Olivier Mailhot, Isabella S Glenn, Seth F Vigneron, Violla Bassim, Xinyu Xu, Karla Fonseca-Valencia, Matthew S Smith, Dmytro S Radchenko, James S Fraser, Yurii S Moroz, John J Irwin, Brian K Shoichet
The impact of Library Size and Scale of Testing on Virtual Screening. bioRxiv : the preprint server for biology (2024)
Rahul K Suryawanshi, Priyadarshini Jaishankar, Galen J Correy, Moira M Rachman, Patrick C O'Leary, Taha Y Taha, Francisco J Zapatero-Belinchón, Maria McCavitt-Malvido, Yagmur Umay Doruk, Maisie G V Stevens, Morgan E Diolati, Manasi P Jogalekar, Alicia L Richards, Mauricio Montano, Julia Rosecrans, Michael A Matthay, Takaya Togo, Ryan L Gonciarz, Saumya Gopalkrishnan, R Jeffrey Neitz, Nevan J Krogan, Danielle L Swaney, Brian K Shoichet, Melanie M Ott, Adam R Renslo, Alan Ashworth, Brian K Shoichet
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2. bioRxiv : the preprint server for biology (2024)
Gabriella O Estevam, Edmond M Linossi, Christian B Macdonald, Carla A Espinoza, Jennifer M Michaud, Willow Coyote-Maestas, Eric A Collisson, Natalia Jura, Brian K Shoichet
Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. eLife 12 (2024)
Donovan D Trinidad, Christian B Macdonald, Oren S Rosenberg, Brian K Shoichet, Willow Coyote-Maestas
Deep mutational scanning of EccD 3 reveals the molecular basis of its essentiality in the mycobacterium ESX secretion system. bioRxiv : the preprint server for biology (2024)
Gabriella O Estevam, Edmond M Linossi, Jingyou Rao, Christian B Macdonald, Ashraya Ravikumar, Karson M Chrispens, Anthony Capra, Willow Coyote-Maestas, Harold Pimentel, Eric A Collisson, Natalia Jura, Brian K Shoichet
Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv : the preprint server for biology (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. eLife 12 (2024)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 12 (2024)
Rahul K Suryawanshi, Priyadarshini Jaishankar, Galen J Correy, Moira M Rachman, Patrick C O'Leary, Taha Y Taha, Francisco J Zapatero-Belinchón, Maria McCavitt-Malvido, Yagmur Umay Doruk, Maisie G V Stevens, Morgan E Diolati, Manasi P Jogalekar, Alicia L Richards, Mauricio Montano, Julia Rosecrans, Michael A Matthay, Takaya Togo, Ryan L Gonciarz, Saumya Gopalkrishnan, R Jeffrey Neitz, Nevan J Krogan, Danielle L Swaney, Brian K Shoichet, Melanie M Ott, Adam R Renslo, Alan Ashworth, Brian K Shoichet
The Mac1 ADP-ribosylhydrolase is a Therapeutic Target for SARS-CoV-2. bioRxiv : the preprint server for biology (2024)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 12 (2024)
Galen J Correy, Moira M Rachman, Takaya Togo, Stefan Gahbauer, Yagmur Umay Doruk, Maisie G V Stevens, Priyadarshini Jaishankar, Brian Kelley, Brian Goldman, Molly Schmidt, Trevor Kramer, Alan Ashworth, Patrick F Riley, Brian K Shoichet, Adam R Renslo, W Patrick Walters, Brian K Shoichet
Extensive exploration of structure activity relationships for the SARS-CoV-2 macrodomain from shape-based fragment merging and active learning. bioRxiv : the preprint server for biology (2024)
Brianna Bibel, Tushar Raskar, Mary Couvillion, Muhoon Lee, Jordan I Kleinman, Nono Takeuchi-Tomita, L Stirling Churchman, Brian K Shoichet, Danica Galonić Fujimori
Context-specific inhibition of mitochondrial ribosomes by phenicol and oxazolidinone antibiotics. bioRxiv : the preprint server for biology (2024)
Gabriella O Estevam, Edmond M Linossi, Jingyou Rao, Christian B Macdonald, Ashraya Ravikumar, Karson M Chrispens, Anthony Capra, Willow Coyote-Maestas, Harold Pimentel, Eric A Collisson, Natalia Jura, Brian K Shoichet
Mapping kinase domain resistance mechanisms for the MET receptor tyrosine kinase via deep mutational scanning. bioRxiv : the preprint server for biology (2024)
Stephanie A Wankowicz, Brian K Shoichet
Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCrJ 11 (Pt 4) (2024)
Stephanie A Wankowicz, Brian K Shoichet
Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCrJ 11 (Pt 4) (2024)
Fangyu Liu, Olivier Mailhot, Isabella S Glenn, Seth F Vigneron, Violla Bassim, Xinyu Xu, Karla Fonseca-Valencia, Matthew S Smith, Dmytro S Radchenko, James S Fraser, Yurii S Moroz, John J Irwin, Brian K Shoichet
The impact of Library Size and Scale of Testing on Virtual Screening. bioRxiv : the preprint server for biology (2024)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake Riley, Akshay Raju, Daniel W Hogan, Jessica Flowers, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Automated multiconformer model building for X-ray crystallography and cryo-EM. eLife 12 (2024)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Siyuan Du, Stephanie A Wankowicz, Filip Yabukarski, Tzanko I Doukov, Daniel Herschlag, Brian K Shoichet
Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv : the preprint server for biology (2023)
Abhinaya Venkatesan, Pablo D Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman, Kayla Dunn, James Bryant Collins, Brian K Shoichet, Erik C Andersen, Ray M Kaplan, John S Gilleard
Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS pathogens 19 (3) (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
David C Wych, Phillip C Aoto, Lily Vu, Alexander M Wolff, David L Mobley, Brian K Shoichet, Susan S Taylor, Michael E Wall
Molecular-dynamics simulation methods for macromolecular crystallography. Acta crystallographica. Section D, Structural biology 79 (Pt 1) (2023)
Abhinaya Venkatesan, Pablo D Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman, Kayla Dunn, James Bryant Collins, Brian K Shoichet, Erik C Andersen, Ray M Kaplan, John S Gilleard
Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS pathogens 19 (3) (2023)
Andreas Varkaris, Ermira Pazolli, Hakan Gunaydin, Qi Wang, Levi Pierce, Alessandro A Boezio, Lucian DiPietro, Adam Frost, Fabrizio Giordanetto, Erika Paige Hamilton, Katherine Harris, Michael J Holliday, Tamieka L Hunter, Amanda Iskandar, Yongli Ji, Alexandre Larivée, Jonathan R LaRochelle, Andre Lescarbeau, Fabien Llambi, Brenda Lormil, Mary M Mader, Brenton G Mar, Iain Martin, Thomas H McLean, Klaus Michelsen, Yakov Pechersky, Erika G Puente, Ramin Samadani, Alison M Schram, Kelley Shortsleeves, Sweta Swaminathan, Shahein Tajmir, Gege Tan, Yong Tang, Roberto Valverde, Bryan Wehrenberg, Jeremy Wilbur, Bret R Williams, Hongtao Zeng, W Patrick Walters, Beni B Wolf, David E Shaw, Donald A Bergstrom, James Watters, Brian K Shoichet, Pascal D Fortin, D Randal Kipp
Discovery and clinical proof-of-concept of RLY-2608, a first-in-class mutant-selective allosteric PI3Ka inhibitor that decouples anti-tumor activity from hyperinsulinemia. Cancer discovery (2023)
Stephanie A Wankowicz, Ashraya Ravikumar, Shivani Sharma, Blake T Riley, Akshay Raju, Daniel W Hogan, Henry van den Bedem, Daniel A Keedy, Brian K Shoichet
Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM. bioRxiv : the preprint server for biology (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Abhinaya Venkatesan, Pablo D Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman, Kayla Dunn, James Bryant Collins, Brian K Shoichet, Erik C Andersen, Ray M Kaplan, John S Gilleard
Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS pathogens 19 (3) (2023)
David C Wych, Phillip C Aoto, Lily Vu, Alexander M Wolff, David L Mobley, Brian K Shoichet, Susan S Taylor, Michael E Wall
Molecular-dynamics simulation methods for macromolecular crystallography. Acta crystallographica. Section D, Structural biology 79 (Pt 1) (2023)
Gabriella O Estevam, Edmond M Linossi, Christian B Macdonald, Carla A Espinoza, Jennifer M Michaud, Willow Coyote-Maestas, Eric A Collisson, Natalia Jura, Brian K Shoichet
Conserved regulatory motifs in the juxtamembrane domain and kinase N-lobe revealed through deep mutational scanning of the MET receptor tyrosine kinase domain. bioRxiv : the preprint server for biology (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Alexander M Wolff, Eriko Nango, Iris D Young, Aaron S Brewster, Minoru Kubo, Takashi Nomura, Michihiro Sugahara, Shigeki Owada, Benjamin A Barad, Kazutaka Ito, Asmit Bhowmick, Sergio Carbajo, Tomoya Hino, James M Holton, Dohyun Im, Lee J O'Riordan, Tomoyuki Tanaka, Rie Tanaka, Raymond G Sierra, Fumiaki Yumoto, Kensure Tono, So Iwata, Nicholas K Sauter, Brian K Shoichet, Michael C Thompson
Mapping protein dynamics at high spatial resolution with temperature-jump X-ray crystallography. Nature chemistry (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Do-Hyun Kim, Yilin Wang, Haerin Jung, Rachael L Field, Xinya Zhang, Ta-Chiang Liu, Changqing Ma, Brian K Shoichet, Jonathan Robert Brestoff, Steven J Van Dyken
A type 2 immune circuit in the stomach controls mammalian adaptation to dietary chitin. Science (New York, N.Y.) 381 (6662) (2023)
Siyuan Du, Stephanie A Wankowicz, Filip Yabukarski, Tzanko I Doukov, Daniel Herschlag, Brian K Shoichet
Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv : the preprint server for biology (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2. Proceedings of the National Academy of Sciences of the United States of America 120 (2) (2023)
Siyuan Du, Stephanie A Wankowicz, Filip Yabukarski, Tzanko I Doukov, Daniel Herschlag, Brian K Shoichet
Refinement of Multiconformer Ensemble Models from Multi-temperature X-ray Diffraction Data. bioRxiv : the preprint server for biology (2023)
Taha Y Taha, Rahul K Suryawanshi, Irene P Chen, Galen J Correy, Patrick C O'Leary, Manasi P Jogalekar, Maria McCavitt-Malvido, Morgan Diolaiti, Gabriella R Kimmerly, Chia-Lin Tsou, Luis Martinez- Sobrido, Nevan J Krogan, Alan Ashworth, Brian K Shoichet, Melanie Ott
A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo . bioRxiv : the preprint server for biology (2023)
Abhinaya Venkatesan, Pablo D Jimenez Castro, Arianna Morosetti, Hannah Horvath, Rebecca Chen, Elizabeth Redman, Kayla Dunn, James Bryant Collins, Brian K Shoichet, Erik C Andersen, Ray M Kaplan, John S Gilleard
Molecular evidence of widespread benzimidazole drug resistance in Ancylostoma caninum from domestic dogs throughout the USA and discovery of a novel β-tubulin benzimidazole resistance mutation. PLoS pathogens 19 (3) (2023)
Roberto Efraín Díaz, Andrew K Ecker, Galen J Correy, Pooja Asthana, Iris D Young, Bryan Faust, Michael C Thompson, Ian B Seiple, Steven J Van Dyken, Richard M Locksley, Brian K Shoichet
Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase. bioRxiv : the preprint server for biology (2023)
David C Wych, Phillip C Aoto, Lily Vu, Alexander M Wolff, David L Mobley, Brian K Shoichet, Susan S Taylor, Michael E Wall
Molecular-dynamics simulation methods for macromolecular crystallography. Acta crystallographica. Section D, Structural biology 79 (Pt 1) (2023)
Célia M Guérin, Audrey Vinchent, Marie Fernandes, Isabelle Damour, Agathe Laratte, Rémi Tellier, Gabriella O Estevam, Jean-Pascal Meneboo, Céline Villenet, Clotilde Descarpentries, Brian K Shoichet, Martin Figeac, Alexis B Cortot, Etienne Rouleau, David Tulasne
MET variants with activating N-lobe mutations identified in hereditary papillary renal cell carcinomas still require ligand stimulation. bioRxiv : the preprint server for biology (2023)
Galen J Correy, Daniel W Kneller, Gwyndalyn Phillips, Swati Pant, Silvia Russi, Aina E Cohen, George Meigs, James M Holton, Stefan Gahbauer, Michael C Thompson, Alan Ashworth, Leighton Coates, Andrey Y Kovalevsky, Flora Meilleur, Brian K Shoichet
The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. Science advances 8 (21) (2022)
Filip Yabukarski, Tzanko I Doukov, Margaux M Pinney, Justin T Biel, Brian K Shoichet, Daniel Herschlag
Ensemble-function relationships to dissect mechanisms of enzyme catalysis. Science advances 8 (41) (2022)
Kaitlyn Tsai, Vanja Stojković, D John Lee, Iris D Young, Teresa Szal, Dorota Klepacki, Nora Vazquez-Laslop, Alexander S Mankin, Brian K Shoichet, Danica Galonić Fujimori
Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics. Nature structural & molecular biology 29 (2) (2022)
Kaitlyn Tsai, Vanja Stojković, Lianet Noda-Garcia, Iris D Young, Alexander G Myasnikov, Jordan I Kleinman, Ali Palla, Stephen N Floor, Adam Frost, Brian K Shoichet, Dan S Tawfik, Danica Galonić Fujimori
Directed evolution of the rRNA methylating enzyme Cfr reveals molecular basis of antibiotic resistance. eLife 11 (2022)
Manfred S Weiss, Jan Wollenhaupt, Galen J Correy, Brian K Shoichet, Andreas Heine, Gerhard Klebe, Tobias Krojer, Marjolein Thunissen, Nicholas M Pearce
Of problems and opportunities-How to treat and how to not treat crystallographic fragment screening data. Protein science : a publication of the Protein Society 31 (9) (2022)
Stephanie A Wankowicz, Saulo H de Oliveira, Daniel W Hogan, Henry van den Bedem, Brian K Shoichet
Ligand binding remodels protein side-chain conformational heterogeneity. eLife 11 (2022)
Cody Krivacic, Kale Kundert, Xingjie Pan, Roland A Pache, Lin Liu, Shane O Conchúir, Jeliazko R Jeliazkov, Jeffrey J Gray, Michael C Thompson, Brian K Shoichet, Tanja Kortemme
Accurate positioning of functional residues with robotics-inspired computational protein design. Proceedings of the National Academy of Sciences of the United States of America 119 (11) (2022)
Jennifer M Michaud, Ali Madani, Brian K Shoichet
A language model beats alphafold2 on orphans. Nature biotechnology 40 (11) (2022)
Stefan Gahbauer, Galen J Correy, Marion Schuller, Matteo P Ferla, Yagmur Umay Doruk, Moira M Rachman, Taiasean Wu, Morgan E Diolati, Siyi Wang, R Jeffrey Neitz, Daren Fearon, Dmytro S Radchenko, Yurii S Moroz, John J Irwin, Adam R Renslo, Jenny C Taylor, Jason E Gestwicki, Frank von Delft, Alan Ashworth, Ivan Ahel, Brian K Shoichet, Brian K Shoichet
Structure-based inhibitor optimization for the Nsp3 Macrodomain of SARS-CoV-2. bioRxiv : the preprint server for biology (2022)
Vijay Jayaraman, D John Lee, Nadav Elad, Shay Vimer, Michal Sharon, Brian K Shoichet, Dan S Tawfik
A counter-enzyme complex regulates glutamate metabolism in Bacillus subtilis. Nature chemical biology 18 (2) (2021)
Catherine L Lawson, Andriy Kryshtafovych, Paul D Adams, Pavel V Afonine, Matthew L Baker, Benjamin A Barad, Paul S Bond, Tom Burnley, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Ken A Dill, Frank DiMaio, Daniel P Farrell, Brian K Shoichet, Mark A Herzik, Soon Wen Hoh, Jie Hou, Li-Wei Hung, Maxim Igaev, Agnel-Praveen Joseph, Daisuke Kihara, Dilip Kumar, Sumit Mittal, Bohdan Monastyrskyy, Mateusz Olek, Colin M Palmer, Ardan Patwardhan, Alberto Perez, Jonas Pfab, Grigore D Pintilie, Jane S Richardson, Peter B Rosenthal, Daipayan Sarkar, Luisa U Schäfer, Michael F Schmid, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Genki Terashi, Thomas C Terwilliger, Andrea C Vaiana, Liguo Wang, Zhe Wang, Stephanie A Wankowicz, Christopher J Williams, Martyn David Winn, Tianqi Wu, Xiaodi Yu, Kaiming Zhang, Helen M Berman, Wah Chiu
Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge. Nature methods 18 (2) (2021)
Willow Coyote-Maestas, Brian K Shoichet
ORACLE reveals a bright future to fight bacteria. eLife 10 (2021)
Meghna Gupta, Caleigh M Azumaya, Michelle Moritz, Sergei Pourmal, Amy Diallo, Gregory E Merz, Gwendolyn M Jang, Mehdi Bouhaddou, Andrea Fossati, Axel F Brilot, Devan Diwanji, Evelyn Hernandez, Nadia Herrera, Huong T Kratochvil, Victor L Lam, Fei Li, Yang Li, Henry C Nguyen, Carlos A Nowotny, Tristan W Owens, Jessica K Peters, Alexandrea N Rizo, Ursula Schulze-Gahmen, Amber M Smith, Iris D Young, Zanlin Yu, Daniel E Asarnow, Christian B Billesbølle, Melody G Campbell, Jen Chen, Kuei-Ho Chen, Un Seng Chio, Miles Sasha Dickinson, Loan Doan, Mingliang Jin, Sun Kyung Kim, Junrui Li, Grant J Jensen, Edmond M Linossi, Yanxin Liu, Megan Lo, Jocelyne Lopez, Kyle E Lopez, Adamo S Mancino, Frank R Moss, Michael D Paul, Komal Ishwar Pawar, Adrian Pelin, Thomas H Pospiech, Cristina Puchades, Soumya Govinda Remesh, Maliheh Safari, Kaitlin Schaefer, Ming Sun, Mariano C Tabios, Aye C Thwin, Erron W Titus, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Kaihua Zhang, Sunny Zhang, Jianhua Zhao, Fengbo Zhou, Yuan Zhou, Lorena Zuliani-Alvarez, null null, David A Agard, Yifan Cheng, Brian K Shoichet, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R Southworth, Robert M Stroud, Danielle L Swaney, Nevan J Krogan, Adam Frost, Oren S Rosenberg, Kliment A Verba
CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. bioRxiv : the preprint server for biology (2021)
Marion Schuller, Galen J Correy, Stefan Gahbauer, Daren Fearon, Taiasean Wu, Roberto Efraín Díaz, Iris D Young, Luan Carvalho Martins, Dominique H Smith, Ursula Schulze-Gahmen, Tristan W Owens, Ishan Deshpande, Gregory E Merz, Aye C Thwin, Justin T Biel, Jessica K Peters, Michelle Moritz, Nadia Herrera, Huong T Kratochvil, null null, Anthony Aimon, James M Bennett, José Brandão-Neto, Aina E Cohen, Alexandre Dias, Alice Douangamath, Louise Dunnett, Oleg Fedorov, Matteo P Ferla, Martin R Fuchs, Tyler J Gorrie-Stone, James M Holton, Michael G Johnson, Tobias Krojer, George Meigs, Ailsa J Powell, Johannes Gregor Matthias Rack, Victor L Rangel, Silvia Russi, Rachael E Skyner, Clyde A Smith, Alexei S Soares, Jennifer L Wierman, Kang Zhu, Peter O'Brien, Natalia Jura, Alan Ashworth, John J Irwin, Michael C Thompson, Jason E Gestwicki, Frank von Delft, Brian K Shoichet, Brian K Shoichet, Ivan Ahel
Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking. Science advances 7 (16) (2021)
Hannes Braberg, Ignacia Echeverria, Stefan Bohn, Peter Cimermancic, Anthony L Shiver, Richard Alexander, Jiewei Xu, Michael Shales, Raghuvar Dronamraju, Shuangying Jiang, Gajendradhar Dwivedi, Derek Bogdanoff, Kaitlin K Chaung, Ruth Hüttenhain, Shuyi Wang, David Mavor, Riccardo Pellarin, Dina Schneidman-Duhovny, Joel S Bader, Brian K Shoichet, John H Morris, James E Haber, Brian D Strahl, Carol A Gross, Jun-Biao Dai, Jef D Boeke, Andrej Sali, Nevan J Krogan
Genetic interaction mapping informs integrative structure determination of protein complexes. Science (New York, N.Y.) 370 (6522) (2021)
Brian K Shoichet, Kresten Lindorff-Larsen, Massimiliano Bonomi
What Will Computational Modeling Approaches Have to Say in the Era of Atomistic Cryo-EM Data? Journal of chemical information and modeling 60 (5) (2020)
Blake T Riley, Stephanie A Wankowicz, Saulo H P de Oliveira, Gydo C P van Zundert, Daniel W Hogan, Brian K Shoichet, Daniel A Keedy, Henry van den Bedem
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps. Protein science : a publication of the Protein Society 30 (1) (2020)
Filip Yabukarski, Justin T Biel, Margaux M Pinney, Tzanko I Doukov, Alexander S Powers, Brian K Shoichet, Daniel Herschlag
Assessment of enzyme active site positioning and tests of catalytic mechanisms through X-ray-derived conformational ensembles. Proceedings of the National Academy of Sciences of the United States of America 117 (52) (2020)
Anum Azam Glasgow, Yao-Ming Huang, Daniel J Mandell, Michael C Thompson, Ryan Ritterson, Amanda L Loshbaugh, Jenna Pellegrino, Cody Krivacic, Roland A Pache, Kyle A Barlow, Noah Ollikainen, Deborah Jeon, Mark J S Kelly, Brian K Shoichet, Tanja Kortemme
Computational design of a modular protein sense-response system. Science (New York, N.Y.) 366 (6468) (2020)
Benjamin A Barad, Lin Liu, Roberto E Diaz, Ralp Basilio, Steven J Van Dyken, Richard M Locksley, Brian K Shoichet
Differences in the chitinolytic activity of mammalian chitinases on soluble and insoluble substrates. Protein science : a publication of the Protein Society 29 (4) (2020)
David E Gordon, Gwendolyn M Jang, Mehdi Bouhaddou, Jiewei Xu, Kirsten Obernier, Kris M White, Matthew J O'Meara, Veronica V Rezelj, Jeffrey Z Guo, Danielle L Swaney, Tia A Tummino, Ruth Hüttenhain, Robyn M Kaake, Alicia L Richards, Beril Tutuncuoglu, Helene Foussard, Jyoti Batra, Kelsey Haas, Maya Modak, Minkyu Kim, Paige Haas, Benjamin J Polacco, Hannes Braberg, Jacqueline M Fabius, Manon Eckhardt, Margaret Soucheray, Melanie J Bennett, Merve Cakir, Michael J McGregor, Qiongyu Li, Bjoern Meyer, Ferdinand Roesch, Thomas Vallet, Alice Mac Kain, Lisa Miorin, Elena Moreno, Zun Zar Chi Naing, Yuan Zhou, Shiming Peng, Ying Shi, Ziyang Zhang, Wenqi Shen, Ilsa T Kirby, James E Melnyk, John S Chorba, Kevin Lou, Shizhong A Dai, Inigo Barrio-Hernandez, Danish Memon, Claudia Hernandez-Armenta, Jiankun Lyu, Christopher J P Mathy, Tina Perica, Kala Bharath Pilla, Sai J Ganesan, Daniel J Saltzberg, Ramachandran Rakesh, Xi Liu, Sara Brin Rosenthal, Lorenzo Calviello, Srivats Venkataramanan, José M Liboy-Lugo, Yizhu Lin, Xi-Ping Huang, YongFeng Liu, Stephanie A Wankowicz, Markus Bohn, Maliheh Safari, Fatima S Ugur, Cassandra Koh, Nastaran Sadat Savar, Quang Dinh Tran, Djoshkun Shengjuler, Sabrina J Fletcher, Michael C O'Neal, Yiming Cai, Jason C J Chang, David J Broadhurst, Saker Klippsten, Phillip P Sharp, Nicole A Wenzell, Duygu Kuzuoglu-Ozturk, Hao-Yuan Wang, Raphael Trenker, Janet M Young, Devin A Cavero, Joseph Hiatt, Theodore L Roth, Ujjwal Rathore, Advait Subramanian, Julia Noack, Mathieu Hubert, Robert M Stroud, Alan D Frankel, Oren S Rosenberg, Kliment A Verba, David A Agard, Melanie Ott, Michael Emerman, Natalia Jura, Mark Von Zastrow, Eric Verdin, Alan Ashworth, Olivier Schwartz, Christophe D'Enfert, Shaeri Mukherjee, Matthew P Jacobson, Harmit Singh Malik, Danica G Fujimori, Trey Ideker, Charles S Craik, Stephen N Floor, Brian K Shoichet, John D Gross, Andrej Sali, Bryan L Roth, Davide Ruggero, Jack Taunton, Tanja Kortemme, Pedro Beltrao, Marco Vignuzzi, Adolfo García-Sastre, Kevan M Shokat, Brian K Shoichet, Nevan J Krogan
A SARS-CoV-2 protein interaction map reveals targets for drug repurposing. Nature 583 (7816) (2020)
Xingjie Pan, Michael C Thompson, Sunny Zhang, Lin Liu, Brian K Shoichet, Mark J S Kelly, Tanja Kortemme
Expanding the space of protein geometries by computational design of de novo fold families. Science (New York, N.Y.) 369 (6507) (2020)
Alexander M Wolff, Iris D Young, Raymond G Sierra, Aaron S Brewster, Michael W Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmick, Justin T Biel, Sergio Carbajo, Aina E Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D Koralek, Minoru Kubo, Tomas S Lazarou, Takashi Nomura, Shigeki Owada, Avi J Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M Thompson, Henry van den Bedem, Rahel A Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensure Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K Sauter, Brian K Shoichet, Michael C Thompson
Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals. IUCrJ 7 (Pt 2) (2020)
Aron Broom, Rojo V Rakotoharisoa, Michael C Thompson, Niayesh Zarifi, Erin Nguyen, Nurzhan Mukhametzhanov, Lin Liu, Brian K Shoichet, Roberto A Chica
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico. Nature communications 11 (1) (2020)
David E Gordon, Joseph Hiatt, Mehdi Bouhaddou, Veronica V Rezelj, Svenja Ulferts, Hannes Braberg, Alexander S Jureka, Kirsten Obernier, Jeffrey Z Guo, Jyoti Batra, Robyn M Kaake, Andrew R Weckstein, Tristan W Owens, Meghna Gupta, Sergei Pourmal, Erron W Titus, Merve Cakir, Margaret Soucheray, Michael J McGregor, Zeynep Cakir, Gwendolyn M Jang, Matthew J O'Meara, Tia A Tummino, Ziyang Zhang, Helene Foussard, Ajda Rojc, Yuan Zhou, Dmitry Kuchenov, Ruth Hüttenhain, Jiewei Xu, Manon Eckhardt, Danielle L Swaney, Jacqueline M Fabius, Manisha Ummadi, Beril Tutuncuoglu, Ujjwal Rathore, Maya Modak, Paige Haas, Kelsey M Haas, Zun Zar Chi Naing, Ernst H Pulido, Ying Shi, Inigo Barrio-Hernandez, Danish Memon, Eirini Petsalaki, Alistair S Dunham, Miguel Correa Marrero, David Francis Burke, Cassandra Koh, Thomas Vallet, Jesus A Silvas, Caleigh M Azumaya, Christian B Billesbølle, Axel F Brilot, Melody G Campbell, Amy Diallo, Miles Sasha Dickinson, Devan Diwanji, Nadia Herrera, Nicholas Hoppe, Huong T Kratochvil, Yanxin Liu, Gregory E Merz, Michelle Moritz, Henry C Nguyen, Carlos A Nowotny, Cristina Puchades, Alexandrea N Rizo, Ursula Schulze-Gahmen, Amber M Smith, Ming Sun, Iris D Young, Jianhua Zhao, Daniel Asarnow, Justin T Biel, Alisa Bowen, Julian R Braxton, Jen Chen, Cynthia M Chio, Un Seng Chio, Ishan Deshpande, Loan Doan, Bryan Faust, Sebastian Flores, Mingliang Jin, Sun Kyung Kim, Victor L Lam, Fei Li, Junrui Li, Grant J Jensen, Yang Li, Xi Liu, Megan Lo, Kyle E Lopez, Arthur A Melo, Frank R Moss, Phuong Nguyen, Joana Paulino, Komal Ishwar Pawar, Jessica K Peters, Thomas H Pospiech, Maliheh Safari, Smriti Sangwan, Kaitlin Schaefer, Paul V Thomas, Aye C Thwin, Raphael Trenker, Eric Tse, Tsz Kin Martin Tsui, Feng Wang, Natalie Whitis, Zanlin Yu, Kaihua Zhang, Sunny Zhang, Fengbo Zhou, Daniel J Saltzberg, null null, Anthony J Hodder, Amber S Shun-Shion, Daniel M Williams, Kris M White, Romel Rosales, Thomas Kehrer, Lisa Miorin, Elena Moreno, Arvind H Patel, Suzannah J Rihn, Mir Mubashir Khalid, Albert Vallejo-Gracia, Parinaz Fozouni, Camille R Simoneau, Theodore L Roth, David Wu, Mohd Anisul Karim, Maya Ghoussaini, Ian Dunham, Francesco Berardi, Sebastian Weigang, Maxime Chazal, Jisoo Park, James P Logue, Marisa E McGrath, Stuart M Weston, Robert E Haupt, C James Hastie, Matthew Elliott, Fiona Brown, Kerry A Burness, Elaine Reid, Mark Dorward, Clare Johnson, Stuart G Wilkinson, Anna Geyer, Daniel M Giesel, Carla Baillie, Samantha Raggett, Hannah Leech, Rachel Toth, Nicola Goodman, Kathleen C Keough, Abigail L Lind, null null, Reyna J Klesh, Kafi R Hemphill, Jared Carlson-Stevermer, Jennifer Oki, Kevin Holden, Travis Maures, Katherine S Pollard, Andrej Sali, David A Agard, Yifan Cheng, Brian K Shoichet, Adam Frost, Natalia Jura, Tanja Kortemme, Aashish Manglik, Daniel R Southworth, Robert M Stroud, Dario R Alessi, Paul Davies, Matthew B Friemann, Trey Ideker, Carmen Abate, Nolwenn Jouvenet, Georg Kochs, Brian K Shoichet, Melanie M Ott, Massimo Palmarini, Kevan M Shokat, Adolfo García-Sastre, Jeremy A Rassen, Robert Grosse, Oren S Rosenberg, Kliment A Verba, Christopher F Basler, Marco Vignuzzi, Andrew A Peden, Pedro Beltrao, Nevan J Krogan
Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.) 370 (6521) (2020)
Qi Li, Jenna Pellegrino, D John Lee, Arthur A Tran, Hector A Chaires, Ruoxi Wang, Jesslyn E Park, Kaijie Ji, David Chow, Na Zhang, Axel F Brilot, Justin T Biel, Gydo van Zundert, Kenneth Borrelli, Dean Shinabarger, Cindy Wolfe, Beverly Murray, Matthew P Jacobson, Estelle Mühle, Olivier Chesneau, Brian K Shoichet, Ian B Seiple
Synthetic group A streptogramin antibiotics that overcome Vat resistance. Nature 586 (7827) (2020)
Michael C Thompson, Benjamin A Barad, Alexander M Wolff, Hyun Sun Cho, Friedrich Schotte, Daniel M C Schwarz, Philip Anfinrud, Brian K Shoichet
Temperature-jump solution X-ray scattering reveals distinct motions in a dynamic enzyme. Nature chemistry 11 (11) (2019)
Julia K Rotow, Philippe Gui, Wei Wu, Victoria M Raymond, Richard B Lanman, Frederic J Kaye, Nir Peled, Ferran Fece de la Cruz, Brandon A Nadres, Ryan B Corcoran, Iwei Yeh, Boris C Bastian, Petr Starostik, Kimberly Newsom, Victor R Olivas, Alexander M Wolff, Brian K Shoichet, Eric A Collisson, Caroline E McCoach, D Ross Camidge, Jose Pacheco, Lyudmila Bazhenova, Tianhong Li, Trever G Bivona, Collin M Blakely
Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research 26 (2) (2019)
David C Wych, Brian K Shoichet, David L Mobley, Michael E Wall
Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein. Structural dynamics (Melville, N.Y.) 6 (6) (2019)
David Mavor, Kyle A Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M Green, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Charlotte A Nelson, Erin M Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice E Ary, David P Bauer, Ian D Bergman, Rachel M Brunetti, Cynthia M Chio, Shizhong A Dai, Miles S Dickinson, Susanna K Elledge, Cole V M Helsell, Nathan L Hendel, Emily Kang, Nadja Kern, Matvei S Khoroshkin, Lisa L Kirkemo, Greyson R Lewis, Kevin Lou, Wesley M Marin, Alison M Maxwell, Peter F McTigue, Douglas Myers-Turnbull, Tamas L Nagy, Andrew M Natale, Keely Oltion, Sergei Pourmal, Gabriel K Reder, Nicholas J Rettko, Peter J Rohweder, Daniel M C Schwarz, Sophia K Tan, Paul V Thomas, Ryan W Tibble, Jason P Town, Mary K Tsai, Fatima S Ugur, Douglas R Wassarman, Alexander M Wolff, Taia S Wu, Derek Bogdanoff, Jennifer Li, Kurt S Thorn, Shane O'Conchúir, Danielle L Swaney, Eric D Chow, Hiten D Madhani, Sy Redding, Daniel N Bolon, Tanja Kortemme, Joseph L DeRisi, Martin Kampmann, Brian K Shoichet
Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance. Biology open 7 (7) (2018)
Renee Otten, Lin Liu, Lillian R Kenner, Michael W Clarkson, David Mavor, Dan S Tawfik, Dorothee Kern, Brian K Shoichet
Rescue of conformational dynamics in enzyme catalysis by directed evolution. Nature communications 9 (1) (2018)
Daniel A Keedy, Zachary B Hill, Justin T Biel, Emily Kang, T Justin Rettenmaier, José Brandão-Neto, Nicholas M Pearce, Frank von Delft, James A Wells, Brian K Shoichet
An expanded allosteric network in PTP1B by multitemperature crystallography, fragment screening, and covalent tethering. eLife 7 (2018)
Jessica L Thomaston, Rahel A Woldeyes, Takanori Nakane, Ayumi Yamashita, Tomoyuki Tanaka, Kotaro Koiwai, Aaron S Brewster, Benjamin A Barad, Yujie Chen, Thomas Lemmin, Monarin Uervirojnangkoorn, Toshi Arima, Jun Kobayashi, Tetsuya Masuda, Mamoru Suzuki, Michihiro Sugahara, Nicholas K Sauter, Rie Tanaka, Osamu Nureki, Kensuke Tono, Yasumasa Joti, Eriko Nango, So Iwata, Fumiaki Yumoto, Brian K Shoichet, William F DeGrado
XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction. Proceedings of the National Academy of Sciences of the United States of America 114 (51) (2017)
Ray Yu-Ruei Wang, Yifan Song, Benjamin A Barad, Yifan Cheng, Brian K Shoichet, Frank Dimaio
Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta. eLife 5 (2016)
Andrew H Van Benschoten, Lin Liu, Ana Gonzalez, Aaron S Brewster, Nicholas K Sauter, Brian K Shoichet, Michael E Wall
Measuring and modeling diffuse scattering in protein X-ray crystallography. Proceedings of the National Academy of Sciences of the United States of America 113 (15) (2016)
David Mavor, Kyle A Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane Ó Conchúir, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, Brian K Shoichet
Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife 5 (2016)
Benjamin A Barad, Nathaniel Echols, Ray Yu-Ruei Wang, Yifan Cheng, Frank DiMaio, Paul D Adams, Brian K Shoichet
EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy. Nature methods 12 (10) (2015)
Henry van den Bedem, Brian K Shoichet
Integrative, dynamic structural biology at atomic resolution--it's about time. Nature methods 12 (4) (2015)
Daniel A Keedy, Lillian R Kenner, Matthew Warkentin, Rahel A Woldeyes, Jesse B Hopkins, Michael C Thompson, Aaron S Brewster, Andrew H Van Benschoten, Elizabeth L Baxter, Monarin Uervirojnangkoorn, Scott E McPhillips, Jinhu Song, Roberto Alonso-Mori, James M Holton, William I Weis, Axel T Brunger, S Michael Soltis, Henrik Lemke, Ana Gonzalez, Nicholas K Sauter, Aina E Cohen, Henry van den Bedem, Robert E Thorne, Brian K Shoichet
Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 4 (2015)

Brian K Shoichet.css-eqlu8i{font-size:small;padding-left:4px;} (James S Fraser)

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Brian K Shoichet (James S Fraser)