J
Jerome Eberhardt
Researcher at Scripps Research Institute
Publications - 15
Citations - 1192
Jerome Eberhardt is an academic researcher from Scripps Research Institute. The author has contributed to research in topics: AutoDock & Druggability. The author has an hindex of 8, co-authored 14 publications receiving 265 citations. Previous affiliations of Jerome Eberhardt include Scripps Health & French Institute of Health and Medical Research.
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Journal ArticleDOI
AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings.
TL;DR: This work implemented Python bindings to facilitate scripting and the development of docking workflows in AutoDock Vina 1.2.0, an effort toward the unification of the features of the autoDock4 and AutoD Dock Vina docking engines.
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Allostery in Its Many Disguises: From Theory to Applications
Shoshana J. Wodak,Emanuele Paci,Nikolay V. Dokholyan,Nikolay V. Dokholyan,Igor N. Berezovsky,Amnon Horovitz,Jing Li,Vincent J. Hilser,Ivet Bahar,John Karanicolas,Gerhard Stock,Peter Hamm,Roland H. Stote,Jerome Eberhardt,Yassmine Chebaro,Annick Dejaegere,Marco Cecchini,Jean-Pierre Changeux,Peter G. Bolhuis,Jocelyne Vreede,Pietro Faccioli,Simone Orioli,Riccardo Ravasio,Le Yan,Carolina Brito,Matthieu Wyart,Paraskevi Gkeka,Ivan Rivalta,Giulia Palermo,Giulia Palermo,J. Andrew McCammon,Joanna Panecka-Hofman,Rebecca C. Wade,Rebecca C. Wade,Antonella Di Pizio,Masha Y. Niv,Ruth Nussinov,Chung-Jung Tsai,Hyunbum Jang,Dzmitry Padhorny,Dima Kozakov,Tom McLeish +41 more
TL;DR: An overview of the progress and remaining limitations in the understanding of the mechanistic foundations of allostery gained from computational and experimental analyses of real protein systems and model systems is provided.
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Structural Insights into the Molecular Mechanism of Vitamin D Receptor Activation by Lithocholic Acid Involving a New Mode of Ligand Recognition
Anna Y. Belorusova,Jerome Eberhardt,Noelle Potier,Roland H. Stote,Annick Dejaegere,Natacha Rochel +5 more
TL;DR: Biological activity assays, structural analysis, and molecular dynamics simulations indicate that the recognition of two ligand molecules is crucial for VDR agonism by LCA, and the unique binding mode of LCA provides clues for the development of new chemical compounds that target alternative binding sites for therapeutic applications.
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Comparison of affinity ranking using AutoDock-GPU and MM-GBSA scores for BACE-1 inhibitors in the D3R Grand Challenge 4
Léa El Khoury,Diogo Santos-Martins,Sukanya Sasmal,Jerome Eberhardt,Giulia Bianco,Francesca Alessandra Ambrosio,Francesca Alessandra Ambrosio,Leonardo Solis-Vasquez,Andreas Koch,Stefano Forli,David L. Mobley +10 more
TL;DR: The MM-GBSA protocol is sensitive to details in the protein-ligand system and neutral ligands are more adapted to MM- GBSA calculations than charged ligands, and predicted binding affinities depend on the initial conformation of the BACE-1 receptor.
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Structural Basis of Altered Potency and Efficacy Displayed by a Major in Vivo Metabolite of the Antidiabetic PPARγ Drug Pioglitazone
Sarah A. Mosure,Jinsai Shang,Jerome Eberhardt,Richard Brust,Jie Zheng,Patrick R. Griffin,Stefano Forli,Douglas J. Kojetin +7 more
TL;DR: Results indicating that Pio hydroxylation affects its potency and efficacy as a PParγ agonist contributes to the understanding of PPARγ-drug metabolite interactions.