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ORCIDFelice C. Lightstone
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2020 – today
- 2023
[j12]Martin Stroet
, Bertrand Caron, Martin S. Engler, Jimi van der Woning, Aude Kauffmann, Marc van Dijk, Mohammed El-Kebir, Koen Visscher, Josef Holownia, Callum Macfarlane, Brian J. Bennion, Svetlana Gelpi-Dominguez, Felice C. Lightstone, Tijs van der Storm, Daan P. Geerke, Alan E. Mark, Gunnar W. Klau:
OFraMP: a fragment-based tool to facilitate the parametrization of large molecules. J. Comput. Aided Mol. Des. 37(8): 357-371 (2023)- [j11]Garrett A. Stevenson, Dan Kirshner, Brian J. Bennion, Yue Yang, Xiaohua Zhang, Adam T. Zemla, Marisa W. Torres, Aidan Epstein, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Sergio Ernesto Wong, Jonathan E. Allen, Felice C. Lightstone:
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method. J. Chem. Inf. Model. 63(21): 6655-6666 (2023) - 2022
- [j10]Harsh Bhatia, Jayaraman J. Thiagarajan, Rushil Anirudh, T. S. Jayram, Tomas Oppelstrup, Helgi I. Ingólfsson, Felice C. Lightstone, Peer-Timo Bremer:
A biology-informed similarity metric for simulated patches of human cell membrane. Mach. Learn. Sci. Technol. 3(3): 35010 (2022) - [c5]Dong H. Ahn, Xiaohua Zhang, Jeffrey Mast, Stephen Herbein, Francesco Di Natale, Dan Kirshner, Sam Ade Jacobs, Ian Karlin, Daniel J. Milroy, Bronis R. de Supinski, Brian Van Essen, Jonathan E. Allen, Felice C. Lightstone:
Scalable Composition and Analysis Techniques for Massive Scientific Workflows. e-Science 2022: 32-43 - [i5]Konstantia Georgouli, Helgi I. Ingólfsson, Fikret Aydin, Mark Heimann, Felice C. Lightstone, Peer-Timo Bremer, Harsh Bhatia:
Emerging Patterns in the Continuum Representation of Protein-Lipid Fingerprints. CoRR abs/2207.04333 (2022) - [i4]Fikret Aydin, Konstantia Georgouli, Gautham Dharuman, James N. Glosli, Felice C. Lightstone, Helgi I. Ingólfsson, Peer-Timo Bremer, Harsh Bhatia:
Identifying Orientation-specific Lipid-protein Fingerprints using Deep Learning. CoRR abs/2207.06630 (2022) - [i3]Ya Ju Fan, Jonathan E. Allen, Kevin S. McLoughlin, Da Shi, Brian J. Bennion, Xiaohua Zhang, Felice C. Lightstone:
Evaluating Point-Prediction Uncertainties in Neural Networks for Drug Discovery. CoRR abs/2210.17043 (2022) - 2021
- [j9]Sam Ade Jacobs, Tim Moon, Kevin McLoughlin, Derek Jones, David Hysom, Dong H. Ahn, John C. Gyllenhaal, Pythagoras Watson, Felice C. Lightstone, Jonathan E. Allen, Ian Karlin, Brian Van Essen:
Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models. Int. J. High Perform. Comput. Appl. 35(5) (2021) - [j8]Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam T. Zemla, Garrett Stevenson, W. F. Drew Bennett, Daniel A. Kirshner, Sergio Ernesto Wong, Felice C. Lightstone, Jonathan E. Allen:
Improved Protein-Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. J. Chem. Inf. Model. 61(4): 1583-1592 (2021) - [j7]Harsh Bhatia, Timothy S. Carpenter, Helgi I. Ingólfsson, Gautham Dharuman, Piyush Karande, Shusen Liu, Tomas Oppelstrup, Chris Neale, Felice C. Lightstone, Brian Van Essen, James N. Glosli, Peer-Timo Bremer:
Machine-learning-based dynamic-importance sampling for adaptive multiscale simulations. Nat. Mach. Intell. 3(5): 401-409 (2021) - [c4]Harsh Bhatia, Francesco Di Natale, Joseph Y. Moon, Xiaohua Zhang, Joseph R. Chavez, Fikret Aydin, Christopher B. Stanley, Tomas Oppelstrup, Chris Neale, Sara Kokkila Schumacher, Dong H. Ahn, Stephen Herbein, Timothy S. Carpenter, Sandrasegaram Gnanakaran, Peer-Timo Bremer, James N. Glosli, Felice C. Lightstone, Helgi I. Ingólfsson:
Generalizable coordination of large multiscale workflows: challenges and learnings at scale. SC 2021: 10 - [c3]Garrett A. Stevenson, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Brian J. Bennion, Monica Borucki, Feliza Bourguet, Aidan Epstein, Magdalena Franco, Brooke Harmon, Stewart He, Max P. Katz, Daniel A. Kirshner, Victoria Lao, Edmond Y. Lau, Jacky Lo, Kevin McLoughlin, Richard Mosesso, Deepa K. Murugesh, Oscar A. Negrete, Edwin A. Saada, Brent Segelke, Maxwell Stefan, Marisa W. Torres, Dina Weilhammer, Sergio Ernesto Wong, Yue Yang, Adam T. Zemla, Xiaohua Zhang, Fangqiang Zhu, Felice C. Lightstone, Jonathan E. Allen:
High-throughput virtual screening of small molecule inhibitors for SARS-CoV-2 protein targets with deep fusion models. SC 2021: 74 - [i2]Garrett A. Stevenson, Derek Jones, Hyojin Kim, W. F. Drew Bennett, Brian J. Bennion, Monica Borucki, Feliza Bourguet, Aidan Epstein, Magdalena Franco, Brooke Harmon, Stewart He, Max P. Katz, Daniel A. Kirshner, Victoria Lao, Edmond Y. Lau, Jacky Lo, Kevin McLoughlin, Richard Mosesso, Deepa K. Murugesh, Oscar A. Negrete, Edwin A. Saada, Brent Segelke, Maxwell Stefan, Marisa W. Torres, Dina Weilhammer, Sergio Ernesto Wong, Yue Yang, Adam T. Zemla, Xiaohua Zhang, Fangqiang Zhu, Felice C. Lightstone, Jonathan E. Allen:
High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models. CoRR abs/2104.04547 (2021) - 2020
- [j6]Fangqiang Zhu, Xiaohua Zhang, Jonathan E. Allen, Derek Jones, Felice C. Lightstone:
Binding Affinity Prediction by Pairwise Function Based on Neural Network. J. Chem. Inf. Model. 60(6): 2766-2772 (2020) - [j5]W. F. Drew Bennett, Stewart He, Camille L. Bilodeau, Derek Jones, Delin Sun, Hyojin Kim, Jonathan E. Allen, Felice C. Lightstone, Helgi I. Ingólfsson:
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning. J. Chem. Inf. Model. 60(11): 5375-5381 (2020) - [i1]Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam T. Zemla, Garrett Stevenson, William D. Bennett, Dan Kirshner, Sergio Ernesto Wong, Felice C. Lightstone, Jonathan E. Allen:
Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. CoRR abs/2005.07704 (2020)
2010 – 2019
- 2019
- [c2]Francesco Di Natale, Harsh Bhatia, Timothy S. Carpenter, Chris Neale, Sara Kokkila Schumacher, Tomas Oppelstrup, Liam Stanton, Xiaohua Zhang, Shiv Sundram, Thomas R. W. Scogland, Gautham Dharuman, Michael P. Surh, Yue Yang, Claudia Misale, Lars Schneidenbach, Carlos H. A. Costa, Changhoan Kim, Bruce D'Amora, Sandrasegaram Gnanakaran, Dwight V. Nissley, Frederick H. Streitz, Felice C. Lightstone, Peer-Timo Bremer, James N. Glosli, Helgi I. Ingólfsson:
A massively parallel infrastructure for adaptive multiscale simulations: modeling RAS initiation pathway for cancer. SC 2019: 57:1-57:16 - 2016
- [j4]Timothy S. Carpenter, Felice C. Lightstone:
An Electrostatic Funnel in the GABA-Binding Pathway. PLoS Comput. Biol. 12(4) (2016) - 2015
- [c1]Xiaohua Zhang, Horacio Pérez Sánchez, Felice C. Lightstone:
Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach. IWBBIO (2) 2015: 584-593 - 2014
- [j3]Xiaohua Zhang, Sergio Ernesto Wong, Felice C. Lightstone:
Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment. J. Chem. Inf. Model. 54(1): 324-337 (2014) - 2013
- [j2]Xiaohua Zhang, Sergio Ernesto Wong, Felice C. Lightstone:
Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines. J. Comput. Chem. 34(11): 915-927 (2013) - [j1]Daniel A. Kirshner, Jerome P. Nilmeier, Felice C. Lightstone:
Catalytic site identification - a web server to identify catalytic site structural matches throughout PDB. Nucleic Acids Res. 41(Webserver-Issue): 256-265 (2013)
Coauthor Index
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