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Author Details

Rommie E Amaro
University of California
2001
207
45
Christopher Churas (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36175661Targeted protein S-nitrosylation of ACE2 inhibits SARS-CoV-2 infection.Nat Chem Biol2023
38023523QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chem Sci2023
37794035Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.Nat Commun2023
37601331Multiscale computational modeling of the effects of 2'-deoxy-ATP on cardiac muscle calcium handling.J Appl Phys2023
37191169Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications.J Chem Inf Model2023
37023323Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations.J Chem Inf Model2023
36989354Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors.Sci Adv2023
37077408SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx.Cell Rep Phys Sci2023
37396863Revealing the Impacts of Chemical Complexity on Submicrometer Sea Spray Aerosol Morphology.ACS Cent Sci2023
36923917APOBEC3A Catalytic Inactivity Mutation Induces Tertiary Structure Destabilization.ACS Med Chem Lett2023
36719802DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling.J Chem Theory Comput2023
36647365#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.Int J High Perform Comput Appl2023
35165203Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.Proc Natl Acad Sci U S A2022
35411336Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection.bioRxiv2022
35759413SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.J Chem Inf Model2022
35783295CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.Nat Rev Chem2022
37013054Inhibition of PRMT5 by market drugs as a novel cancer therapeutic avenue.Genes Dis2022
36589893Breathing and Tilting: Mesoscale Simulations Illuminate Influenza Glycoprotein Vulnerabilities.ACS Cent Sci2022
36567670Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry.J Chem Inf Model2022
35895977Gaussian Accelerated Molecular Dynamics in OpenMM.J Phys Chem B2022
35926454Spike-heparan sulfate interactions in SARS-CoV-2 infection.Curr Opin Struct Biol2022
35924341Words Matter: On the Debate over Free Speech, Inclusivity, and Academic Excellence.J Phys Chem Lett2022
35982678Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitors.bioRxiv2022
35982676Breathing and tilting: mesoscale simulations illuminate influenza glycoprotein vulnerabilities.bioRxiv2022
35922510Architecture and self-assembly of the jumbo bacteriophage nuclear shell.Nature2022
35948006Discovery of compounds that reactivate p53 mutants in vitro and in vivo.Cell Chem Biol2022
35320719Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates.Cell Rep2022
35204684Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations.Biomolecules2022
35199221Benchmarking ensemble docking methods in D3R Grand Challenge 4.J Comput Aided Mol Des2022
35106370<i>GlycoGrip</i>: Cell Surface-Inspired Universal Sensor for Betacoronaviruses.ACS Cent Sci2022
35324217Amino Acids Are Driven to the Interface by Salts and Acidic Environments.J Phys Chem Lett2022
32975902OCRE Domains of Splicing Factors RBM5 and RBM10: Tyrosine Ring-Flip Frequencies Determined by Integrated Use of <sup>1</sup> H NMR Spectroscopy and Molecular Dynamics Simulations.Chembiochem2021
33872011Development of Dimethylisoxazole-Attached Imidazo[1,2-<i>a</i>]pyridines as Potent and Selective CBP/P300 Inhibitors.J Med Chem2021
33821277Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN.bioRxiv2021
33619492A glycan gate controls opening of the SARS-CoV-2 spike protein.bioRxiv2021
33921405Structural Characterization of a Minimal Antibody against Human APOBEC3B.Viruses2021
33558528Incorporation of sensing modalities into de novo designed fluorescence-activating proteins.Nat Commun2021
33609494A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors.Biophys J2021
33661099Disease-related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveal a path to selective inhibitors.Elife2021
34668709Advancing Women in Chemistry.J Chem Inf Model2021
34816263#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.bioRxiv2021
34844409Gaussian-Accelerated Molecular Dynamics with the Weighted Ensemble Method: A Hybrid Method Improves Thermodynamic and Kinetic Sampling.J Chem Theory Comput2021
34686332Derlin rhomboid pseudoproteases employ substrate engagement and lipid distortion to enable the retrotranslocation of ERAD membrane substrates.Cell Rep2021
34417349SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma.Proc Natl Acad Sci U S A2021
34413500A glycan gate controls opening of the SARS-CoV-2 spike protein.Nat Chem2021
33939913Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease.J Chem Inf Model2021
34321356Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes.Proc Natl Acad Sci U S A2021
34212944A critical overview of computational approaches employed for COVID-19 drug discovery.Chem Soc Rev2021
34318808Calcium bridging drives polysaccharide co-adsorption to a proxy sea surface microlayer.Phys Chem Chem Phys2021
34024101Cation-Driven Lipopolysaccharide Morphological Changes Impact Heterogeneous Reactions of Nitric Acid with Sea Spray Aerosol Particles.J Phys Chem Lett2021
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Collaborators

James Andrew McCammon
Co-authored papers 28
Robert V Swift
University of California San Diego
Co-authored papers 18
Jacob D Durrant
University of Pittsburgh
Co-authored papers 18
Victoria A Feher
University of California San Diego
Co-authored papers 11
Reuben S Harris
University of Texas Health San Antonio
Co-authored papers 11
Michael K Gilson
University of California
Co-authored papers 6
Jason S McLellan
Co-authored papers 6
Michael A Carpenter
University of Minnesota
Co-authored papers 5
Jeffrey R Wagner
Kaiser Permanente San Francisco Medical Center
Co-authored papers 5
William L Brown
University of Minnesota
Co-authored papers 5
Ilkay Altintas
Halicioglu Data Science Institute, University of California San Diego
Co-authored papers 5
Dong Xu
University of Missouri
Co-authored papers 4
Michael Chiu
University of California
Co-authored papers 4
Michael J Holst
Co-authored papers 4
Andrew D McCulloch
University of California
Co-authored papers 4
Daniel A Harki
University of Minnesota
Co-authored papers 4
Ian A Wilson
The Scripps Research Institute, USA The Skaggs Institute for Chemical Biology
Co-authored papers 4
Lillian T Chong
Co-authored papers 4
Stephen K Burley
The State University of New Jersey
Co-authored papers 4
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The State University of New Jersey
Co-authored papers 3
Shuai Liu
XtalPi Inc.
Co-authored papers 3
Chenghua Shao
The State University of New Jersey
Co-authored papers 3
Susan S Taylor
University of California
Co-authored papers 2
Swagata Ghatak
National Institute of Science Education and Research
Co-authored papers 2
Gregory M Goldgof
University of California san francisco
Co-authored papers 2
Tomohiro Nakamura
The Scripps Research Institute
Co-authored papers 2
Willy Wriggers
Old Dominion University
Co-authored papers 2
Stuart A Lipton
The Scripps Research Institute, University of California
Co-authored papers 2
Chengjin Ye
Texas Biomedical Research Institute
Co-authored papers 2
Partho Ghosh
University of California
Co-authored papers 2
Release 1.2