Author

D. E. Shaw

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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Biophysics· 9 Biochemistry· 1 Cell Biology· 1

Signature Assays, Organisms & Methods

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Research Focus:protein folding & dynamics· 6 Approach:biophysical modeling· 4 Assay:protein structure· 3 Assay:structural biology· 3 Organism:virus· 3 Research Focus:drug response / drug discovery· 2 Approach:experimental assay· 2 Approach:mechanistic / dynamical model· 2

Frequent Co-Authors

A. C. Pan· 3 shared Q. Wang· 3 shared B. Malone· 2 shared C. Y. Yeh· 2 shared E. A. Campbell· 2 shared E. Llewellyn· 2 shared E. T. Eng· 2 shared F. Giordanetto· 2 shared

Activity by Year

2018-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 20 mutual co-author links

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3 shared papersBiophysics

A. C. Pan

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Author profile →

11 papers

Recent·Most cited

A conserved local structural motif controls the kinetics of PTP1B catalysis

C. Y. Yeh, J. A. Izaguirre, J. B. Greisman, L. Willmore, P. Maragakis, D. E. Shaw

This study identifies the PDFG motif as a conserved structural switch controlling WPD-loop conformational transitions in PTP1B, essential for catalytic activity.

bioRxiv · Feb 28, 2023 · PreprintBiophysics

Discovery and validation of the binding poses of allosteric fragment hits to PTP1b: From molecular dynamics simulations to X-ray crystallography

J. B. Greisman, L. Willmore, C. Y. Yeh, F. Giordanetto, S. Shahamadtar, H. Nisonoff, P. Maragakis, D. E. Shaw

The paper uses molecular dynamics simulations to predict fragment binding poses to PTP1b, which are later validated by X-ray crystallography.

bioRxiv · Nov 14, 2022 · PreprintBiophysics

Characterizing receptor flexibility to predict mutations that lead to human adaptation of influenza hemagglutinin

H. Xu, T. Palpant, C. Weinberger, D. E. Shaw

The paper uses molecular dynamics simulations to predict mutations in influenza hemagglutinin that enhance binding to human sialic acid receptors, validated by experiments.

Journal of Chemical Theory and Computation · Aug 9, 2022Peer-reviewedBiophysics

Ensemble cryo-electron microscopy reveals conformational states of the nsp13 helicase in the SARS-CoV-2 helicase replication-transcription complex

J. Chen, Q. Wang, B. Malone, E. Llewellyn, Y. Pechersky, K. Maruthi, E. T. Eng, J. K. Perry, E. A. Campbell, D. E. Shaw, S. A. Darst

This study uses cryo-EM and simulations to identify four conformational states of the nsp13 helicase in the SARS-CoV-2 RTC, revealing an allosteric mechanism for switching between RNA synthesis and backtracking.

bioRxiv · Nov 10, 2021 · PreprintBiophysics

How does a small molecule bind at a cryptic binding site?

Y. Shan, V. P. Mysore, A. E. Leffler, E. T. Kim, S. Sagawa, D. E. Shaw

This study uses molecular dynamics simulations and free energy perturbation to identify and characterize small molecule binding at cryptic sites in protein-protein interactions.

bioRxiv · Mar 31, 2021Biophysics

Structural basis for backtracking by the SARS-CoV-2 replication-transcription complex

B. Malone, J. Chen, Q. Wang, E. Llewellyn, Y. J. Choi, P. D. B. Olinares, X. Cao, C. Hernandez, E. T. Eng, B. T. Chait, D. E. Shaw, R. Landick, S. A. Darst, E. A. Campbell

This paper shows that SARS-CoV-2 RdRp undergoes backtracking, which may aid proofreading and antiviral resistance.

bioRxiv · Mar 13, 2021Biochemistry

Molecular basis of small-molecule binding to α-synuclein

P. Robustelli, A. Ibanez-de-Opakua, C. Campbell-Bezat, F. Giordanetto, S. Becker, M. Zweckstetter, A. C. Pan, D. E. Shaw

The paper uses molecular dynamics simulations to study small-molecule binding to α-synuclein, revealing dynamic interactions that align with experimental data.

bioRxiv · Jan 22, 2021Biophysics

Lysyl oxidase-like 2 (LOXL2) is Increased in Asthma and Contributes to Asthmatic Airway Remodelling

J. Ramis, R. Middlewick, F. Pappalardo, J. T. Cairns, I. D. Stewart, A. E. John, S.-u. Naveed, R. Krishnan, S. Miller, D. E. Shaw, C. E. Brightling, L. Buttery, F. R. Rose, G. Jenkins, S. R. Johnson, A. L. Tatler

This study shows LOXL2 is increased in asthma and contributes to airway remodelling by enhancing TGFβ activation and ECM stiffness.

bioRxiv · Nov 16, 2020 · PreprintCell Biology

The mechanism of coupled folding-upon-binding of an intrinsically disordered protein

P. Robustelli, S. Piana, D. E. Shaw

The paper describes the atomic-level mechanism of folding-upon-binding for an intrinsically disordered protein using molecular dynamics simulations.

bioRxiv · Mar 23, 2020Biophysics

Structural mechanism for Bruton’s tyrosine kinase activation at the cell membrane

Q. Wang, Y. Pechersky, S. Sagawa, A. C. Pan, D. E. Shaw

This study uses molecular dynamics simulations to show that PIP3 stabilizes Btk dimerization at the cell membrane, which is critical for Btk activation.

bioRxiv · Apr 18, 2018Biophysics

Atomic-level characterization of protein-protein association

A. C. Pan, D. Jacobson, K. Yatsenko, D. Sritharan, T. M. Weinreich, D. E. Shaw

The paper uses molecular dynamics simulations to study protein-protein association mechanisms, finding that native associations often involve dissociation and re-association near the native interface rather than extensive interfacial exploration.

bioRxiv · Apr 17, 2018Biophysics