Rommie E. Amaro

Publication Activity (10 Years)

Years Active: 2008-2023
Publications (10 Years): 39

Top Topics

Virtual Screening

Computational Chemistry

Grand Challenge

Simulation Data

Top Venues

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

PLoS Comput. Biol.

Publications

Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, A. Sofia F. Oliveira, Clare Morris, Anthony T. Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, S. Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders S. Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai K. Sirumalla, Michael O'connor, Frederick R. Manby, Anima Anandkumar, David J. Hardy, James C. Phillips, Abraham C. Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John D. McCalpin, Christopher J. Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E. Stone, Daniel M. Zuckerman, Adrian J. Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37 (1) (2023)
Anupam Anand Ojha, Ambuj Srivastava, Lane W. Votapka, Rommie E. Amaro
Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J. Chem. Inf. Model. 63 (8) (2023)
Rommie E. Amaro, Jiunn-Yeu Chen, Javier M. Duarte, Thomas E. Hutton, Christopher Irving, Martin C. Kandes, Amit Majumdar, Dmitry Y. Mishin, Mai H. Nguyen, Paul Rodríguez, Fernando Silva, Robert S. Sinkovits, Shawn M. Strande, Mahidhar Tatineni, Leon Si Tran, Nicole Wolter
Voyager - An Innovative Computational Resource for Artificial Intelligence & Machine Learning Applications in Science and Engineering. PEARC (2023)
Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.
Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J. Chem. Inf. Model. 63 (11) (2023)
Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. J. Chem. Inf. Model. 62 (24) (2022)
Lane W. Votapka, Andrew M. Stokely, Anupam A. Ojha, Rommie E. Amaro
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J. Chem. Inf. Model. 62 (13) (2022)
Jessie Low Gan, Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, Rommie E. Amaro, Christopher T. Lee
Benchmarking ensemble docking methods in D3R Grand Challenge 4. J. Comput. Aided Mol. Des. 36 (2) (2022)
Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
Advancing Women in Chemistry. J. Chem. Inf. Model. 61 (11) (2021)
Lorenzo Casalino, Abigail C. Dommer, Zied Gaieb, Emília P. Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony T. Bogetti, Austin Clyde, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian T. Chong, Carlos Simmerling, David J. Hardy, Julio D. C. Maia, James C. Phillips, Thorsten Kurth, Abraham C. Stern, Lei Huang, John D. McCalpin, Mahidhar Tatineni, Tom Gibbs, John E. Stone, Shantenu Jha, Arvind Ramanathan, Rommie E. Amaro
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 35 (5) (2021)
Terra Sztain, Rommie E. Amaro, James Andrew McCammon
Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J. Chem. Inf. Model. 61 (7) (2021)
Adrian J. Mulholland, Rommie E. Amaro
COVID19 - Computational Chemists Meet the Moment. J. Chem. Inf. Model. 60 (12) (2020)
Rommie E. Amaro, Adrian J. Mulholland
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. J. Chem. Inf. Model. 60 (6) (2020)
Rommie E. Amaro, Adrian J. Mulholland
Biomolecular Simulations in the Time of COVID-19, and After. Comput. Sci. Eng. 22 (6) (2020)
Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael Holst, Padmini Rangamani
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. 16 (4) (2020)
Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 60 (12) (2020)
Conor D. Parks, Zied Gaieb, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Johanna M. Jansen, Georgia B. McGaughey, Richard A. Lewis, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 34 (2) (2020)
Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.
Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J. Chem. Inf. Model. 60 (7) (2020)
Michael K. Gilson, Rommie E. Amaro
Drug Design Data Resource, Grand Challenge 4, second of two issues. J. Comput. Aided Mol. Des. 34 (2) (2020)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
Faces of Contemporary CryoEM Information and Modeling. J. Chem. Inf. Model. 60 (5) (2020)
Surl-Hee Ahn, Benjamin R. Jagger, Rommie E. Amaro
Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. J. Chem. Inf. Model. 60 (11) (2020)
Zied Gaieb, Conor D. Parks, Michael Chiu, Huanwang Yang, Chenghua Shao, W. Patrick Walters, Millard H. Lambert, Neysa Nevins, Scott D. Bembenek, Michael K. Ameriks, Tara Mirzadegan, Stephen K. Burley, Rommie E. Amaro, Michael K. Gilson
D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J. Comput. Aided Mol. Des. 33 (1) (2019)
Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. ACM Trans. Math. Softw. 45 (3) (2019)
Jeffrey R. Wagner, Özlem Demir, Michael A. Carpenter, Hideki Aihara, Daniel A. Harki, Reuben S. Harris, Rommie E. Amaro
Determinants of Oligonucleotide Selectivity of APOBEC3B. J. Chem. Inf. Model. 59 (5) (2019)
Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
A Celebration of Women in Computational Chemistry. J. Chem. Inf. Model. 59 (5) (2019)
Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
Frontiers in CryoEM Modeling. J. Chem. Inf. Model. 59 (7) (2019)
Pei-Chi Yang, Shweta Purawat, Pek U. Ieong, Mao-Tsuen Jeng, Kevin R. DeMarco, Igor Vorobyov, Andrew D. McCulloch, Ilkay Altintas, Rommie E. Amaro, Colleen E. Clancy
A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PLoS Comput. Biol. 15 (3) (2019)
Zied Gaieb, Shuai Liu, Symon Gathiaka, Michael Chiu, Huanwang Yang, Chenghua Shao, Victoria A. Feher, W. Patrick Walters, Bernd Kuhn, Markus G. Rudolph, Stephen K. Burley, Michael K. Gilson, Rommie E. Amaro
D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 32 (1) (2018)
Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael Holst
The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. CoRR (2018)
Christopher T. Lee, Rommie E. Amaro
Exascale Computing: A New Dawn for Computational Biology. Comput. Sci. Eng. 20 (5) (2018)
Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
Women in Computational Chemistry. J. Chem. Inf. Model. 58 (11) (2018)
Shweta Purawat, Charles Cowart, Rommie E. Amaro, Ilkay Altintas
Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research. J. Comput. Sci. 20 (2017)
Tavina L. Offutt, Robert V. Swift, Rommie E. Amaro
Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. J. Chem. Inf. Model. 56 (10) (2016)
Shweta Purawat, Charles Cowart, Rommie E. Amaro, Ilkay Altintas
Biomedical Big Data Training Collaborative (BBDTC): An Effort to Bridge the Talent Gap in Biomedical Science and Research. ICCS (2016)
Symon Gathiaka, Shuai Liu, Michael Chiu, Huanwang Yang, Jeanne A. Stuckey, You-Na Kang, Jim Delproposto, Ginger Kubish, James B. Dunbar Jr., Heather A. Carlson, Stephen K. Burley, W. Patrick Walters, Rommie E. Amaro, Victoria A. Feher, Michael K. Gilson
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 30 (9) (2016)
Christopher T. Lee, Jeffrey Comer, Conner Herndon, Nelson Leung, Anna Pavlova, Robert V. Swift, Chris Tung, Christopher N. Rowley, Rommie E. Amaro, Christophe Chipot, Yi Wang, James C. Gumbart
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J. Chem. Inf. Model. 56 (4) (2016)
Robert V. Swift, Siti Azma Jusoh, Tavina L. Offutt, Eric S. Li, Rommie E. Amaro
Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J. Chem. Inf. Model. 56 (5) (2016)
Nur Kusaira Khairul Ikram, Jacob D. Durrant, Muchtaridi Muchtaridi, Ayunni Salihah Zalaludin, Neny Purwitasari, Nornisah Mohamed, Aisyah Saad Abdul Rahim, Chan Kit Lam, Yahaya M. Normi, Noorsaadah Abdul Rahman, Rommie E. Amaro, Habibah A. Wahab
A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. J. Chem. Inf. Model. 55 (2) (2015)
Jacob D. Durrant, Kathryn E. Carlson, Teresa A. Martin, Tavina L. Offutt, Christopher G. Mayne, John A. Katzenellenbogen, Rommie E. Amaro
Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J. Chem. Inf. Model. 55 (9) (2015)
Lane W. Votapka, Rommie E. Amaro
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput. Biol. 11 (10) (2015)
Jacob D. Durrant, Rommie E. Amaro
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinform. 15 (2014)
Pek U. Ieong, Jesper Sørensen, Prasantha L. Vemu, Celia W. Wong, Özlem Demir, Nadya P. Williams, Jianwu Wang, Daniel Crawl, Robert V. Swift, Robert D. Malmstrom, Ilkay Altintas, Rommie E. Amaro
Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations. ICCS (2014)
Jacob D. Durrant, Rommie E. Amaro
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. PLoS Comput. Biol. 10 (7) (2014)
Lane Votapka, Rommie E. Amaro
Multistructural hot spot characterization with FTProd. Bioinform. 29 (3) (2013)
Jiho Park, Luke Czapla, Rommie E. Amaro
Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding. J. Chem. Inf. Model. 53 (8) (2013)
Özlem Demir, Rommie E. Amaro
Mitochondrial RNA Editing Enzyme RET2. J. Chem. Inf. Model. 52 (5) (2012)
Özlem Demir, Roberta Baronio, Faezeh Salehi, Christopher D. Wassman, Linda Hall, G. Wesley Hatfield, Richard Chamberlin, Peter Kaiser, Richard H. Lathrop, Rommie E. Amaro
Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants. PLoS Comput. Biol. 7 (10) (2011)
Robert V. Swift, Rommie E. Amaro
Modeling the pharmacodynamics of passive membrane permeability. J. Comput. Aided Mol. Des. 25 (11) (2011)
Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, James Andrew McCammon
A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 6 (1) (2010)
Rommie E. Amaro, Riccardo Baron, James Andrew McCammon
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. Aided Mol. Des. 22 (9) (2008)