P
Paul Maragakis
Researcher at D. E. Shaw Research
Publications - 37
Citations - 10854
Paul Maragakis is an academic researcher from D. E. Shaw Research. The author has contributed to research in topics: Molecular dynamics & Allosteric regulation. The author has an hindex of 25, co-authored 34 publications receiving 9394 citations. Previous affiliations of Paul Maragakis include University of Strasbourg & Harvard University.
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Journal ArticleDOI
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Kresten Lindorff-Larsen,Stefano Piana,Kim Palmo,Paul Maragakis,John L. Klepeis,Ron O. Dror,David E. Shaw,David E. Shaw +7 more
TL;DR: A new force field, which is termed Amber ff99SB‐ILDN, exhibits considerably better agreement with the NMR data and is validated against a large set of experimental NMR measurements that directly probe side‐chain conformations.
Journal ArticleDOI
Atomic-Level Characterization of the Structural Dynamics of Proteins
David E. Shaw,David E. Shaw,Paul Maragakis,Kresten Lindorff-Larsen,Stefano Piana,Ron O. Dror,Michael P. Eastwood,Joseph A. Bank,John M. Jumper,John K. Salmon,Yibing Shan,Willy Wriggers +11 more
TL;DR: Simulation of the folding of a WW domain showed a well-defined folding pathway and simulation of the dynamics of bovine pancreatic trypsin inhibitor showed interconversion between distinct conformational states.
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Systematic validation of protein force fields against experimental data.
Kresten Lindorff-Larsen,Paul Maragakis,Stefano Piana,Michael P. Eastwood,Ron O. Dror,David E. Shaw,David E. Shaw +6 more
TL;DR: The results suggest that force fields have improved over time, and that the most recent versions, while not perfect, provide an accurate description of many structural and dynamical properties of proteins.
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Pathway and mechanism of drug binding to G-protein-coupled receptors
Ron O. Dror,Albert C. Pan,Daniel H. Arlow,David W. Borhani,Paul Maragakis,Yibing Shan,Huafeng Xu,David E. Shaw,David E. Shaw +8 more
TL;DR: An atomic-level description of the binding process suggests opportunities for allosteric modulation and provides a structural foundation for future optimization of drug–receptor binding and unbinding rates.
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Activation mechanism of the β2-adrenergic receptor
Ron O. Dror,Daniel H. Arlow,Paul Maragakis,Thomas J. Mildorf,Albert C. Pan,Huafeng Xu,David W. Borhani,David E. Shaw +7 more
TL;DR: An activation mechanism for the β2-adrenergic receptor, a prototypical GPCR, is proposed based on atomic-level simulations in which an agonist-bound receptor transitions spontaneously from the active to the inactive crystallographically observed conformation.