David E Shaw

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 43

Top Topics

Molecular Dynamics Simulations

Metastatic Colorectal Cancer

Top Venues

Journal of chemical information and modeling

The Journal of general physiology

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

Journal of medicinal chemistry

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

Publications

Heike Schonherr, Pelin Ayaz, Alexander M Taylor, Jessica B Casaletto, B Barry Toure, Demetri T Moustakas, Brandi M Hudson, Roberto Valverde, Songping Zhao, Patrick J O'Hearn, Lindsey Foster, Dina A Sharon, Sam Garfinkle, Fabrizio Giordanetto, André Lescarbeau, Ravi Kurukulasuriya, Nastaran Gerami-Moayed, Dejan Maglic, Kamil Bruderek, Gaauri Naik, Hakan Gunaydin, Mary M Mader, Alessandro A Boezio, Thomas H McLean, Rongfeng Chen, Yanxia Wang, David E Shaw, James Watters, Donald A Bergstrom
Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Heike Schonherr, Pelin Ayaz, Alexander M Taylor, Jessica B Casaletto, B Barry Toure, Demetri T Moustakas, Brandi M Hudson, Roberto Valverde, Songping Zhao, Patrick J O'Hearn, Lindsey Foster, Dina A Sharon, Sam Garfinkle, Fabrizio Giordanetto, André Lescarbeau, Ravi Kurukulasuriya, Nastaran Gerami-Moayed, Dejan Maglic, Kamil Bruderek, Gaauri Naik, Hakan Gunaydin, Mary M Mader, Alessandro A Boezio, Thomas H McLean, Rongfeng Chen, Yanxia Wang, David E Shaw, James Watters, Donald A Bergstrom
Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Heike Schonherr, Pelin Ayaz, Alexander M Taylor, Jessica B Casaletto, B Barry Toure, Demetri T Moustakas, Brandi M Hudson, Roberto Valverde, Songping Zhao, Patrick J O'Hearn, Lindsey Foster, Dina A Sharon, Sam Garfinkle, Fabrizio Giordanetto, André Lescarbeau, Ravi Kurukulasuriya, Nastaran Gerami-Moayed, Dejan Maglic, Kamil Bruderek, Gaauri Naik, Hakan Gunaydin, Mary M Mader, Alessandro A Boezio, Thomas H McLean, Rongfeng Chen, Yanxia Wang, David E Shaw, James Watters, Donald A Bergstrom
Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Heike Schonherr, Pelin Ayaz, Alexander M Taylor, Jessica B Casaletto, B Barry Toure, Demetri T Moustakas, Brandi M Hudson, Roberto Valverde, Songping Zhao, Patrick J O'Hearn, Lindsey Foster, Dina A Sharon, Sam Garfinkle, Fabrizio Giordanetto, André Lescarbeau, Ravi Kurukulasuriya, Nastaran Gerami-Moayed, Dejan Maglic, Kamil Bruderek, Gaauri Naik, Hakan Gunaydin, Mary M Mader, Alessandro A Boezio, Thomas H McLean, Rongfeng Chen, Yanxia Wang, David E Shaw, James Watters, Donald A Bergstrom
Discovery of lirafugratinib (RLY-4008), a highly selective irreversible small-molecule inhibitor of FGFR2. Proceedings of the National Academy of Sciences of the United States of America 121 (6) (2024)
Vivek Subbiah, Vaibhav Sahai, Dejan Maglic, Kamil Bruderek, B Barry Toure, Songping Zhao, Roberto Valverde, Patrick J O'Hearn, Demetri T Moustakas, Heike Schonherr, Nastaran Gerami-Moayed, Alexander M Taylor, Brandi M Hudson, Damian J Houde, Debjani Pal, Lindsey Foster, Hakan Gunaydin, Pelin Ayaz, Dina A Sharon, Lipika Goyal, Alison M Schram, Suneel D Kamath, Cori Ann Sherwin, Oleg Schmidt-Kittler, Kai Yu Jen, Fabien Ricard, Beni B Wolf, David E Shaw, Donald A Bergstrom, James Watters, Jessica B Casaletto
RLY-4008, the first highly selective FGFR2 inhibitor with activity across FGFR2 alterations and resistance mutations. Cancer discovery (2023)
Alexander M Taylor, Bret R Williams, Fabrizio Giordanetto, Elizabeth H Kelley, André Lescarbeau, Kelley Shortsleeves, Yong Tang, W Patrick Walters, Alfonso Arrazate, Christine Bowman, Erin Brophy, Emily W Chan, Gauri Deshmukh, Jack B Greisman, Thomas L Hunsaker, D Randal Kipp, Pablo Saenz Lopez-Larrocha, Danilo Maddalo, Iain J Martin, Paul Maragakis, Mark Merchant, Mark Murcko, Hunter M Nisonoff, Vi Nguyen, Vy Nguyen, Olivia Orozco, Christopher Owen, Levi Pierce, Molly Schmidt, David E Shaw, Sherri Smith, Eric Therrien, John C Tran, Jim Watters, Nigel J Waters, Jeremy Wilbur, Lindsay Willmore
Identification of GDC-1971 (RLY-1971), a SHP2 Inhibitor Designed for the Treatment of Solid Tumors. Journal of medicinal chemistry (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling 63 (9) (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling (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)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling 63 (9) (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling 63 (9) (2023)
Jack B Greisman, Lindsay Willmore, Christine Yiwen Yeh, Fabrizio Giordanetto, Sahar Shahamadtar, Hunter Nisonoff, Paul Maragakis, David E Shaw
Discovery and Validation of the Binding Poses of Allosteric Fragment Hits to Protein Tyrosine Phosphatase 1b: From Molecular Dynamics Simulations to X-ray Crystallography. Journal of chemical information and modeling 63 (9) (2023)
Christine Yiwen Yeh, Jesus A Izaguirre, Jack B Greisman, Lindsay Willmore, Paul Maragakis, David E Shaw
A Conserved Local Structural Motif Controls the Kinetics of PTP1B Catalysis. Journal of chemical information and modeling (2023)
Pelin Ayaz, Agatha Lyczek, YiTing Paung, Victoria R Mingione, Roxana E Iacob, Parker W de Waal, John R Engen, Markus A Seeliger, Yibing Shan, David E Shaw
Structural mechanism of a drug-binding process involving a large conformational change of the protein target. Nature communications 14 (1) (2023)
James Chen, Qi Wang, Brandon F Malone, Eliza Llewellyn, Yakov Pechersky, Kashyap Maruthi, Edward T Eng, Jason K Perry, Elizabeth A Campbell, David E Shaw, Seth A Darst
Ensemble cryo-EM reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex. Nature structural & molecular biology 29 (3) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Yibing Shan, Venkatesh P Mysore, Abba E Leffler, Eric T Kim, Shiori Sagawa, David E Shaw
How does a small molecule bind at a cryptic binding site? PLoS computational biology 18 (3) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Maxwell R Tucker, Stefano Piana, Dazhi Tan, Michael V LeVine, David E Shaw
Development of Force Field Parameters for the Simulation of Single- and Double-Stranded DNA Molecules and DNA-Protein Complexes. The journal of physical chemistry. B 126 (24) (2022)
Huafeng Xu, Timothy Palpant, Cody Weinberger, David E Shaw
Characterizing Receptor Flexibility to Predict Mutations That Lead to Human Adaptation of Influenza Hemagglutinin. Journal of chemical theory and computation 18 (8) (2022)
Paul Robustelli, Alain Ibanez-de-Opakua, Cecily Campbell-Bezat, Fabrizio Giordanetto, Stefan Becker, Markus Zweckstetter, Albert C Pan, David E Shaw
Molecular Basis of Small-Molecule Binding to α-Synuclein. Journal of the American Chemical Society 144 (6) (2022)
Vishwanath Jogini, Morten Ø Jensen, David E Shaw
Gating and modulation of an inward-rectifier potassium channel. The Journal of general physiology 155 (2) (2022)
Brandon F Malone, James Chen, Qi Wang, Eliza Llewellyn, Young Joo Choi, Paul Dominic B Olinares, Xinyun Cao, Carolina Hernandez, Edward T Eng, Brian T Chait, David E Shaw, Robert Landick, Seth A Darst, Elizabeth A Campbell
Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex. Proceedings of the National Academy of Sciences of the United States of America 118 (19) (2021)
Alexander G Donchev, Andrew G Taube, Elizabeth Decolvenaere, Cory Hargus, Robert T McGibbon, Ka-Hei Law, Brent A Gregersen, Je-Luen Li, Kim Palmo, Karthik Siva, Michael Bergdorf, John L Klepeis, David E Shaw
Quantum chemical benchmark databases of gold-standard dimer interaction energies. Scientific data 8 (1) (2021)
Venkatesh P Mysore, Zhi-Wei Zhou, Chiara Ambrogio, Lianbo Li, Jonas N Kapp, Chunya Lu, Qi Wang, Maxwell R Tucker, Jeffrey J Okoro, Gabriela Nagy-Davidescu, Xiao-Chen Bai, Andreas Plückthun, Pasi A Janne, Kenneth D Westover, Yibing Shan, David E Shaw
A structural model of a Ras-Raf signalosome. Nature structural & molecular biology 28 (10) (2021)
Christopher Agnew, Pelin Ayaz, Risa Kashima, Hanna S Loving, Prajakta Ghatpande, Jennifer E Kung, Eric S Underbakke, Yibing Shan, David E Shaw, Akiko Hata, Natalia Jura
Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization. Nature communications 12 (1) (2021)
Christos Adamopoulos, Tamer A Ahmed, Maxwell R Tucker, Peter M U Ung, Min Xiao, Zoi Karoulia, Angelo Amabile, Xuewei Wu, Stuart A Aaronson, Celina Ang, Vito W Rebecca, Brian D Brown, Avner Schlessinger, Meenhard Herlyn, Qi Wang, David E Shaw, Poulikos I Poulikakos
Exploiting Allosteric Properties of RAF and MEK Inhibitors to Target Therapy-Resistant Tumors Driven by Oncogenic BRAF Signaling. Cancer discovery 11 (7) (2021)
Xiao-E Yan, Pelin Ayaz, Su-Jie Zhu, Peng Zhao, Ling Liang, Casey H Zhang, Ya-Chuang Wu, Je-Luen Li, Hwan Geun Choi, Xin Huang, Yibing Shan, David E Shaw, Cai-Hong Yun
Structural Basis of AZD9291 Selectivity for EGFR T790M. Journal of medicinal chemistry 63 (15) (2020)
Paul Robustelli, Stefano Piana, David E Shaw
Mechanism of Coupled Folding-upon-Binding of an Intrinsically Disordered Protein. Journal of the American Chemical Society 142 (25) (2020)
Stefano Piana, Paul Robustelli, Dazhi Tan, Songela Chen, David E Shaw
Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. Journal of chemical theory and computation 16 (4) (2020)
Cristian Predescu, Adam K Lerer, Ross A Lippert, Brian Towles, J P Grossman, Robert M Dirks, David E Shaw
The u-series: A separable decomposition for electrostatics computation with improved accuracy. The Journal of chemical physics 152 (8) (2020)
Cristian Predescu, Michael Bergdorf, David E Shaw
Midtown splines: An optimal charge assignment for electrostatics calculations. The Journal of chemical physics 153 (22) (2020)
Paul Maragakis, Hunter Nisonoff, Brian Cole, David E Shaw
A Deep-Learning View of Chemical Space Designed to Facilitate Drug Discovery. Journal of chemical information and modeling 60 (10) (2020)
Siduo Jiang, Miklos Feher, Chris Williams, Brian Cole, David E Shaw
AutoPH4: An Automated Method for Generating Pharmacophore Models from Protein Binding Pockets. Journal of chemical information and modeling 60 (9) (2020)
Fabrizio Giordanetto, Chentian Jin, Lindsay Willmore, Miklos Feher, David E Shaw
Fragment Hits: What do They Look Like and How do They Bind? Journal of medicinal chemistry 62 (7) (2019)
Stefano Piana, David E Shaw
Atomic-Level Description of Protein Folding inside the GroEL Cavity. The journal of physical chemistry. B 122 (49) (2018)
Michael P Bokoch, Hyunil Jo, James R Valcourt, Yoga Srinivasan, Albert C Pan, Sara Capponi, Michael Grabe, Ron O Dror, David E Shaw, William F DeGrado, Shaun R Coughlin
Entry from the Lipid Bilayer: A Possible Pathway for Inhibition of a Peptide G Protein-Coupled Receptor by a Lipophilic Small Molecule. Biochemistry 57 (39) (2018)
Albert C Pan, Huafeng Xu, Timothy Palpant, David E Shaw
Quantitative Characterization of the Binding and Unbinding of Millimolar Drug Fragments with Molecular Dynamics Simulations. Journal of chemical theory and computation 13 (7) (2017)