Rommie E Amaro

Affiliations

Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.

ORCID: http://orcid.org/0000-0002-9275-9553

Publications (13)

Predicting Ligand Binding Kinetics Using a Markovian Milestoning with Voronoi Tessellations Multiscale Approach.

Journal of chemical theory and computation

Avec: Benjamin R Jagger , Anupam A Ojha ,

Simulations support the interaction of the SARS-CoV-2 spike protein with nicotinic acetylcholine receptors.

bioRxiv : the preprint server for biology

Avec: A Sofia F Oliveira , Amaurys Avila Ibarra , Isabel Bermudez , Lorenzo Casalino , Zied Gaieb , Deborah K Shoemark , Timothy Gallagher , Richard B Sessions , Adrian J Mulholland

An Analysis of Proteochemometric and Conformal Prediction Machine Learning Protein-Ligand Binding Affinity Models.

Frontiers in molecular biosciences

Avec: Conor Parks , Zied Gaieb ,

Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach.

Journal of chemical information and modeling

Avec: Surl-Hee Ahn , Benjamin R Jagger ,

An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries.

Biophysical journal

Avec: Christopher T Lee , Justin G Laughlin , John B Moody , J Andrew McCammon , Michael Holst , Padmini Rangamani

SARS-CoV-2 escape

bioRxiv : the preprint server for biology

Avec: Emanuele Andreano , Giulia Piccini , Danilo Licastro , Lorenzo Casalino , Nicole V Johnson , Ida Paciello , Simeone Dal Monego , Elisa Pantano , Noemi Manganaro , Alessandro Manenti , Rachele Manna , Elisa Casa , Inesa Hyseni , Linda Benincasa , Emanuele Montomoli , Jason S McLellan , Rino Rappuoli

The flexibility of ACE2 in the context of SARS-CoV-2 infection.

Biophysical journal

Avec: Emilia P Barros , Lorenzo Casalino , Zied Gaieb , Abigail C Dommer , Yuzhang Wang , Lucy Fallon , Lauren Raguette , Kellon Belfon , Carlos Simmerling ,

Markov state models and NMR uncover an overlooked allosteric loop in p53.

Chemical science

Avec: Emilia P Barros , Özlem Demir , Jenaro Soto , Melanie J Cocco ,

Examining the Effect of Charged Lipids on Mitochondrial Outer Membrane Dynamics Using Atomistic Simulations.

Biomolecules

Avec: Aline A Oliveira , Tomasz Róg , Albérico B F da Silva , Mark S Johnson , Pekka A Postila

Amino Acids Are Driven to the Interface by Salts and Acidic Environments.

The journal of physical chemistry letters

Avec: Kyle J Angle , Christopher M Nowak , Aakash Davasam , Abigail C Dommer , Nicholas A Wauer , Vicki H Grassian

CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding.

Nature reviews. Chemistry

Avec: Suzanne Ackloo , Rima Al-Awar , Cheryl H Arrowsmith , Hatylas Azevedo , Robert A Batey , Yoshua Bengio , Ulrich A K Betz , Cristian G Bologa , John D Chodera , Wendy D Cornell , Ian Dunham , Gerhard F Ecker , Kristina Edfeldt , Aled M Edwards , Michael K Gilson , Claudia R Gordijo , Gerhard Hessler , Alexander Hillisch , Anders Hogner , John J Irwin , Johanna M Jansen , Daniel Kuhn , Andrew R Leach , Alpha A Lee , Uta Lessel , Maxwell R Morgan , John Moult , Ingo Muegge , Tudor I Oprea , Benjamin G Perry , Patrick Riley , Sophie A L Rousseaux , Kumar Singh Saikatendu , Vijayaratnam Santhakumar , Matthieu Schapira , Cora Scholten , Matthew H Todd , Masoud Vedadi , Andrea Volkamer , Timothy M Willson

DeepWEST: Deep Learning of Kinetic Models with the Weighted Ensemble Simulation Toolkit for Enhanced Sampling.

Journal of chemical theory and computation

Avec: Anupam Anand Ojha , Saumya Thakur , Surl-Hee Ahn ,

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE.

bioRxiv : the preprint server for biology

Avec: Joann Chongsaritsinsuk , Alexandra D Steigmeyer , Keira E Mahoney , Mia A Rosenfeld , Taryn M Lucas , Deniz Ince , Fiona L Kearns , Alexandria S Battison , Marie A Hollenhorst , D Judy Shon , Katherine H Tiemeyer , Victor Attah , Catherine Kwon , Carolyn R Bertozzi , Michael J Ferracane , Stacy A Malaker

Réseau de co-auteurs

Lorenzo Casalino 3 collaborations

Zied Gaieb 3 collaborations

Benjamin R Jagger 2 collaborations

Surl-Hee Ahn 2 collaborations

Emilia P Barros 2 collaborations

Abigail C Dommer 2 collaborations

Anupam A Ojha 1 collaboration

A Sofia F Oliveira 1 collaboration

Amaurys Avila Ibarra 1 collaboration

Isabel Bermudez 1 collaboration

Deborah K Shoemark 1 collaboration

Timothy Gallagher 1 collaboration

Richard B Sessions 1 collaboration

Adrian J Mulholland 1 collaboration

Conor Parks 1 collaboration

Christopher T Lee 1 collaboration

Justin G Laughlin 1 collaboration

John B Moody 1 collaboration

J Andrew McCammon 1 collaboration

Michael Holst 1 collaboration

Padmini Rangamani 1 collaboration

Emanuele Andreano 1 collaboration

Giulia Piccini 1 collaboration

Danilo Licastro 1 collaboration

Nicole V Johnson 1 collaboration

Ida Paciello 1 collaboration

Simeone Dal Monego 1 collaboration

Elisa Pantano 1 collaboration

Noemi Manganaro 1 collaboration

Alessandro Manenti 1 collaboration

Rachele Manna 1 collaboration

Elisa Casa 1 collaboration

Inesa Hyseni 1 collaboration

Linda Benincasa 1 collaboration

Emanuele Montomoli 1 collaboration

Jason S McLellan 1 collaboration

Rino Rappuoli 1 collaboration

Yuzhang Wang 1 collaboration

Lucy Fallon 1 collaboration

Lauren Raguette 1 collaboration

Kellon Belfon 1 collaboration

Carlos Simmerling 1 collaboration

Özlem Demir 1 collaboration

Jenaro Soto 1 collaboration

Melanie J Cocco 1 collaboration

Aline A Oliveira 1 collaboration

Tomasz Róg 1 collaboration

Albérico B F da Silva 1 collaboration

Mark S Johnson 1 collaboration

Pekka A Postila 1 collaboration

Kyle J Angle 1 collaboration

Christopher M Nowak 1 collaboration

Aakash Davasam 1 collaboration

Nicholas A Wauer 1 collaboration

Vicki H Grassian 1 collaboration

Suzanne Ackloo 1 collaboration

Rima Al-Awar 1 collaboration

Cheryl H Arrowsmith 1 collaboration

Hatylas Azevedo 1 collaboration

Robert A Batey 1 collaboration

Yoshua Bengio 1 collaboration

Ulrich A K Betz 1 collaboration

Cristian G Bologa 1 collaboration

John D Chodera 1 collaboration

Wendy D Cornell 1 collaboration

Ian Dunham 1 collaboration

Gerhard F Ecker 1 collaboration

Kristina Edfeldt 1 collaboration

Aled M Edwards 1 collaboration

Michael K Gilson 1 collaboration

Claudia R Gordijo 1 collaboration

Gerhard Hessler 1 collaboration

Alexander Hillisch 1 collaboration

Anders Hogner 1 collaboration

John J Irwin 1 collaboration

Johanna M Jansen 1 collaboration

Daniel Kuhn 1 collaboration

Andrew R Leach 1 collaboration

Alpha A Lee 1 collaboration

Uta Lessel 1 collaboration

Maxwell R Morgan 1 collaboration

John Moult 1 collaboration

Ingo Muegge 1 collaboration

Tudor I Oprea 1 collaboration

Benjamin G Perry 1 collaboration

Patrick Riley 1 collaboration

Sophie A L Rousseaux 1 collaboration

Kumar Singh Saikatendu 1 collaboration

Vijayaratnam Santhakumar 1 collaboration

Matthieu Schapira 1 collaboration

Cora Scholten 1 collaboration

Matthew H Todd 1 collaboration

Masoud Vedadi 1 collaboration

Andrea Volkamer 1 collaboration

Timothy M Willson 1 collaboration

Anupam Anand Ojha 1 collaboration

Saumya Thakur 1 collaboration

Joann Chongsaritsinsuk 1 collaboration

Alexandra D Steigmeyer 1 collaboration

Keira E Mahoney 1 collaboration

Mia A Rosenfeld 1 collaboration

Taryn M Lucas 1 collaboration

Deniz Ince 1 collaboration

Fiona L Kearns 1 collaboration

Alexandria S Battison 1 collaboration

Marie A Hollenhorst 1 collaboration

D Judy Shon 1 collaboration

Katherine H Tiemeyer 1 collaboration

Victor Attah 1 collaboration

Catherine Kwon 1 collaboration

Carolyn R Bertozzi 1 collaboration

Michael J Ferracane 1 collaboration

Stacy A Malaker 1 collaboration