Rommie E. Amaro

56 papers Misc 2Journal 53Unranked 1

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening. J. Chem. Inf. Model. Alma C. Castaneda-Leautaud, Ambuj Srivastava, Eunjung Kim, Donghoon Chung, Thomas D. Bannister, Rommie E. Amaro
2026	J	`jnl`	Toward In Situ Dynamics of DNA-Bound Full-Length p53 Tetramer. J. Chem. Inf. Model. Özlem Demir, Emília P. Barros, Rommie E. Amaro
2025	J	`jnl`	Optimal message passing for molecular prediction is simple, attentive and spatial. CoRR Alma C. Castaneda-Leautaud, Rommie E. Amaro
2025	J	`jnl`	Regulatory Interactions between APOBEC3B N- and C-Terminal Domains. J. Chem. Inf. Model. Mac Kevin E. Braza, Özlem Demir, Surl-Hee Ahn, Clare Morris, Carla Calvó-Tusell, Kelly L. McGuire, Bárbara de la Peña Avalos, Michael A. Carpenter, Yanjun Chen, Lorenzo Casalino, Hideki Aihara, Mark A. Herzik, Reuben S. Harris, Rommie E. Amaro
2024	J	`jnl`	Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins. J. Chem. Inf. Model. Fiona L. Kearns, Mia A. Rosenfeld, Rommie E. Amaro
2024	J	`jnl`	Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. J. Chem. Inf. Model. Jie Li, Oufan Zhang, Kunyang Sun, Yingze Wang, Xingyi Guan, Dorian Bagni, Mojtaba Haghighatlari, Fiona L. Kearns, Conor D. Parks, Rommie E. Amaro, Teresa Head-Gordon
2024	J	`jnl`	NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J. Chem. Inf. Model. Andrew M. Stokely, Lane W. Votapka, Marcus T. Hock, Abigail E. Teitgen, James Andrew McCammon, Andrew D. McCulloch, Rommie E. Amaro
2023	J	`jnl`	#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. Abigail C. Dommer, Lorenzo Casalino, Fiona L. Kearns, Mia A. 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 F. Miller III, Shantenu Jha, Arvind Ramanathan, Lillian T. Chong, Rommie E. Amaro
2023	J	`jnl`	Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications. J. Chem. Inf. Model. Thereza A. Soares, Zoe Cournia, Kevin J. Naidoo, Rommie E. Amaro, Habibah A. Wahab, Kenneth M. Merz Jr.
2023	J	`jnl`	Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations. J. Chem. Inf. Model. Anupam Anand Ojha, Ambuj Srivastava, Lane W. Votapka, Rommie E. Amaro
2023	—	`conf`	Voyager - An Innovative Computational Resource for Artificial Intelligence & Machine Learning Applications in Science and Engineering. PEARC 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
2022	J	`jnl`	Benchmarking ensemble docking methods in D3R Grand Challenge 4. J. Comput. Aided Mol. Des. Jessie Low Gan, Dhruv Kumar, Cynthia Chen, Bryn C. Taylor, Benjamin R. Jagger, Rommie E. Amaro, Christopher T. Lee
2022	J	`jnl`	Celebrating Diversity, Equity, Inclusion, and Respect in Computational and Theoretical Chemistry. J. Chem. Inf. Model. Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
2022	J	`jnl`	SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J. Chem. Inf. Model. Lane W. Votapka, Andrew M. Stokely, Anupam Anand Ojha, Rommie E. Amaro
2021	J	`jnl`	AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics. Int. J. High Perform. Comput. Appl. 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
2021	J	`jnl`	Advancing Women in Chemistry. J. Chem. Inf. Model. Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro
2021	J	`jnl`	Elucidation of Cryptic and Allosteric Pockets within the SARS-CoV-2 Main Protease. J. Chem. Inf. Model. Terra Sztain, Rommie E. Amaro, James Andrew McCammon
2020	J	`jnl`	3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael J. Holst, Padmini Rangamani
2020	J	`jnl`	A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. J. Chem. Inf. Model. Rommie E. Amaro, Adrian J. Mulholland
2020	J	`jnl`	Biomolecular Simulations in the Time of COVID-19, and After. Comput. Sci. Eng. Rommie E. Amaro, Adrian J. Mulholland
2020	J	`jnl`	COVID19 - Computational Chemists Meet the Moment. J. Chem. Inf. Model. Adrian J. Mulholland, Rommie E. Amaro
2020	J	`jnl`	D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 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
2020	J	`jnl`	Drug Design Data Resource, Grand Challenge 4, second of two issues. J. Comput. Aided Mol. Des. Michael K. Gilson, Rommie E. Amaro
2020	J	`jnl`	Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. Kenneth M. Merz Jr., Rommie E. Amaro, Zoe Cournia, Matthias Rarey, Thereza A. Soares, Alexander Tropsha, Habibah A. Wahab, Renxiao Wang
2020	J	`jnl`	Faces of Contemporary CryoEM Information and Modeling. J. Chem. Inf. Model. Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
2020	J	`jnl`	Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry. J. Chem. Inf. Model. Angelica Mazzolari, Ariane Nunes-Alves, Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia, Kenneth M. Merz Jr.
2020	J	`jnl`	Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach. J. Chem. Inf. Model. Surl-Hee Ahn, Benjamin R. Jagger, Rommie E. Amaro
2019	J	`jnl`	A Celebration of Women in Computational Chemistry. J. Chem. Inf. Model. Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
2019	J	`jnl`	A demonstration of modularity, reuse, reproducibility, portability and scalability for modeling and simulation of cardiac electrophysiology using Kepler Workflows. PLoS Comput. Biol. 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
2019	J	`jnl`	D3R Grand Challenge 3: blind prediction of protein-ligand poses and affinity rankings. J. Comput. Aided Mol. Des. 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
2019	J	`jnl`	Determinants of Oligonucleotide Selectivity of APOBEC3B. J. Chem. Inf. Model. Jeffrey R. Wagner, Özlem Demir, Michael A. Carpenter, Hideki Aihara, Daniel A. Harki, Reuben S. Harris, Rommie E. Amaro
2019	J	`jnl`	Frontiers in CryoEM Modeling. J. Chem. Inf. Model. Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro
2019	J	`jnl`	The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation. ACM Trans. Math. Softw. Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
2018	J	`jnl`	D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies. J. Comput. Aided Mol. Des. 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
2018	J	`jnl`	Exascale Computing: A New Dawn for Computational Biology. Comput. Sci. Eng. Christopher T. Lee, Rommie E. Amaro
2018	J	`jnl`	The Implementation of the Colored Abstract Simplicial Complex and its Application to Mesh Generation. CoRR Christopher T. Lee, John B. Moody, Rommie E. Amaro, James Andrew McCammon, Michael J. Holst
2018	J	`jnl`	Women in Computational Chemistry. J. Chem. Inf. Model. Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia
2017	J	`jnl`	Biomedical Big Data Training Collaborative (BBDTC): An effort to bridge the talent gap in biomedical science and research. J. Comput. Sci. Shweta Purawat, Charles Cowart, Rommie E. Amaro, Ilkay Altintas
2016	Misc	`conf`	Biomedical Big Data Training Collaborative (BBDTC): An Effort to Bridge the Talent Gap in Biomedical Science and Research. ICCS Shweta Purawat, Charles Cowart, Rommie E. Amaro, Ilkay Altintas
2016	J	`jnl`	D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions. J. Comput. Aided Mol. Des. 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
2016	J	`jnl`	Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations. J. Chem. Inf. Model. Tavina L. Offutt, Robert V. Swift, Rommie E. Amaro
2016	J	`jnl`	Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles. J. Chem. Inf. Model. Robert V. Swift, Siti Azma Jusoh, Tavina L. Offutt, Eric S. Li, Rommie E. Amaro
2016	J	`jnl`	Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J. Chem. Inf. Model. 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
2015	J	`jnl`	A Virtual Screening Approach For Identifying Plants with Anti H5N1 Neuraminidase Activity. J. Chem. Inf. Model. 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
2015	J	`jnl`	Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput. Biol. Lane W. Votapka, Rommie E. Amaro
2015	J	`jnl`	Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands. J. Chem. Inf. Model. Jacob D. Durrant, Kathryn E. Carlson, Teresa A. Martin, Tavina L. Offutt, Christopher G. Mayne, John A. Katzenellenbogen, Rommie E. Amaro
2014	J	`jnl`	LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. PLoS Comput. Biol. Jacob D. Durrant, Rommie E. Amaro
2014	Misc	`conf`	Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations. ICCS 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
2014	J	`jnl`	WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinform. Jacob D. Durrant, Rommie E. Amaro
2013	J	`jnl`	Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding. J. Chem. Inf. Model. Jiho Park, Luke Czapla, Rommie E. Amaro
2013	J	`jnl`	Multistructural hot spot characterization with FTProd. Bioinform. Lane Votapka, Rommie E. Amaro
2012	J	`jnl`	Elements of Nucleotide Specificity in the J. Chem. Inf. Model. Özlem Demir, Rommie E. Amaro
2011	J	`jnl`	Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants. PLoS Comput. Biol. Özlem Demir, Roberta Baronio, Faezeh Salehi, Christopher D. Wassman, Linda Hall, G. Wesley Hatfield, Richard Chamberlin, Peter Kaiser, Richard H. Lathrop, Rommie E. Amaro
2011	J	`jnl`	Modeling the pharmacodynamics of passive membrane permeability. J. Comput. Aided Mol. Des. Robert V. Swift, Rommie E. Amaro
2010	J	`jnl`	A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology. PLoS Comput. Biol. 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
2008	J	`jnl`	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. Aided Mol. Des. Rommie E. Amaro, Riccardo Baron, James Andrew McCammon