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ORCIDRommie E. Amaro
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2020 – today
- 2024
[j48]Fiona L. Kearns
, Mia A. Rosenfeld, Rommie E. Amaro:
Breaking Down the Bottlebrush: Atomically Detailed Structural Dynamics of Mucins. J. Chem. Inf. Model. 64(20): 7949-7965 (2024)- [j47]Andrew M. Stokely, Lane W. Votapka, Marcus T. Hock, Abigail E. Teitgen, James Andrew McCammon, Andrew D. McCulloch, Rommie E. Amaro:
NetSci: A Library for High Performance Biomolecular Simulation Network Analysis Computation. J. Chem. Inf. Model. 64(20): 7966-7976 (2024) - [j46]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:
Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. J. Chem. Inf. Model. 64(24): 9082-9097 (2024) - 2023
- [j45]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:
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. Int. J. High Perform. Comput. Appl. 37(1): 28-44 (2023) - [j44]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): 2469-2482 (2023) - [j43]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): 3227-3229 (2023) - [c3]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: 278-282 - 2022
- [j42]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): 87-99 (2022) - [j41]Lane W. Votapka, Andrew M. Stokely, Anupam Anand Ojha, Rommie E. Amaro:
SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine. J. Chem. Inf. Model. 62(13): 3253-3262 (2022) - [j40]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): 6287-6291 (2022) - 2021
- [j39]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) - [j38]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): 3495-3501 (2021) - [j37]Zoe Cournia, Thereza A. Soares, Habibah A. Wahab, Rommie E. Amaro:
Advancing Women in Chemistry. J. Chem. Inf. Model. 61(11): 5305-5306 (2021) - 2020
- [j36]Rommie E. Amaro, Adrian J. Mulholland:
Biomolecular Simulations in the Time of COVID-19, and After. Comput. Sci. Eng. 22(6): 30-36 (2020) - [j35]Michael K. Gilson, Rommie E. Amaro:
Drug Design Data Resource, Grand Challenge 4, second of two issues. J. Comput. Aided Mol. Des. 34(2): 97 (2020) - [j34]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): 99-119 (2020) - [j33]Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro:
Faces of Contemporary CryoEM Information and Modeling. J. Chem. Inf. Model. 60(5): 2407-2409 (2020) - [j32]Rommie E. Amaro, Adrian J. Mulholland:
A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19. J. Chem. Inf. Model. 60(6): 2653-2656 (2020) - [j31]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): 3328-3330 (2020) - [j30]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): 5340-5352 (2020) - [j29]Adrian J. Mulholland, Rommie E. Amaro:
COVID19 - Computational Chemists Meet the Moment. J. Chem. Inf. Model. 60(12): 5724-5726 (2020) - [j28]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): 5868-5869 (2020) - [j27]Christopher T. Lee, Justin G. Laughlin, Nils Angliviel de La Beaumelle, Rommie E. Amaro, James Andrew McCammon, Ravi Ramamoorthi, Michael J. Holst, Padmini Rangamani:
3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries. PLoS Comput. Biol. 16(4) (2020)
2010 – 2019
- 2019
- [j26]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): 1-18 (2019) - [j25]Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
A Celebration of Women in Computational Chemistry. J. Chem. Inf. Model. 59(5): 1683-1692 (2019) - [j24]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): 2264-2273 (2019) - [j23]Giulia Palermo, Yuji Sugita, Willy Wriggers, Rommie E. Amaro:
Frontiers in CryoEM Modeling. J. Chem. Inf. Model. 59(7): 3091-3093 (2019) - [j22]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) - [j21]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): 28:1-28:20 (2019) - 2018
- [j20]Christopher T. Lee, Rommie E. Amaro:
Exascale Computing: A New Dawn for Computational Biology. Comput. Sci. Eng. 20(5): 18-25 (2018) - [j19]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): 1-20 (2018) - [j18]Habibah A. Wahab, Rommie E. Amaro, Zoe Cournia:
Women in Computational Chemistry. J. Chem. Inf. Model. 58(11): 2175-2177 (2018) - [i1]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. CoRR abs/1807.01417 (2018) - 2017
- [j17]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: 205-214 (2017) - 2016
- [j16]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): 651-668 (2016) - [j15]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): 721-733 (2016) - [j14]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): 830-842 (2016) - [j13]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): 1923-1935 (2016) - [c2]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: 1791-1800 - 2015
- [j12]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): 308-316 (2015) - [j11]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): 1953-1961 (2015) - [j10]Lane W. Votapka, Rommie E. Amaro:
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j9]Jacob D. Durrant, Rommie E. Amaro:
WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets. BMC Bioinform. 15: 159 (2014) - [j8]Jacob D. Durrant, Rommie E. Amaro:
LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry. PLoS Comput. Biol. 10(7) (2014) - [c1]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: 1745-1755 - 2013
- [j7]Lane Votapka, Rommie E. Amaro:
Multistructural hot spot characterization with FTProd. Bioinform. 29(3): 393-394 (2013) - [j6]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): 2047-2056 (2013) - 2012
- [j5]Özlem Demir, Rommie E. Amaro:
Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2. J. Chem. Inf. Model. 52(5): 1308-1318 (2012) - 2011
- [j4]Robert V. Swift, Rommie E. Amaro:
Modeling the pharmacodynamics of passive membrane permeability. J. Comput. Aided Mol. Des. 25(11): 1007-1017 (2011) - [j3]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) - 2010
- [j2]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)
2000 – 2009
- 2008
- [j1]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): 693-705 (2008)
Coauthor Index
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