Sotabase

Career

· Professor Of Biology, University of California, San Diego (Current)2023–
· Professor Of Chemistry, UC San Diego2016–2023
· Bachelor of Science Chemical Engineering, University of Illinois Urbana-Champaign

Publications (333)

Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein
ACS Central Science · 2020
601
cited
Ensemble Docking in Drug Discovery.
Biophysical Journal · 2018
377
cited
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
J. Comput. Aided Mol. Des. · 2008
317
cited
Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein
bioRxiv · 2020
295
cited
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
bioRxiv · 2020
258
cited
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
Nature Structural &Molecular Biology · 2016
225
cited
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
Nature Communications · 2013
215
cited
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
Chemical Reviews · 2016
213
cited
A glycan gate controls opening of the SARS-CoV-2 spike protein
Nature Chemistry · 2021
211
cited
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
Journal of Chemical Theory and Computation · 2014
210
cited
POVME 3.0: Software for Mapping Binding Pocket Flexibility.
Journal of Chemical Theory and Computation · 2017
205
cited
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
Journal of Chemical Information and Modeling · 2016
190
cited
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
Journal of Computer-Aided Molecular Design · 2016
178
cited
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
Proceedings of the National Academy of Sciences of the United States of America · 2021
178
cited
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Journal of Computer-Aided Molecular Design · 2017
167
cited
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics
bioRxiv · 2020
163
cited
Exploring residue component contributions to dynamical network models of allostery.
Journal of Chemical Theory and Computation · 2012
161
cited
Weighted Implementation of Suboptimal Paths (WISP): An Optimized Algorithm and Tool for Dynamical Network Analysis
Journal of Chemical Theory and Computation · 2014
160
cited
A multiscale coarse-grained model of the SARS-CoV-2 virion
bioRxiv · 2020
156
cited
Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors
bioRxiv · 2022
155
cited
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Rommie Amaro | Researcher Profile | Sotabase | Sotabase