Felice C. Lightstone

Publication Activity (10 Years)

Years Active: 2013-2023
Publications (10 Years): 18

Top Topics

Virtual Screening

Molecular Dynamics

Top Venues

J. Chem. Inf. Model.

Mach. Learn. Sci. Technol.

Publications

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) (2023)
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) (2023)
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 (2022)
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 (2022)
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 (2022)
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) (2022)
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)
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)
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 E. 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)
Harsh Bhatia, Francesco Di Natale, Joseph Y. Moon, Xiaohua Zhang, Joseph R. Chavez, Fikret Aydin, Chris 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)
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 E. 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 (2021)
Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam T. Zemla, Garrett Stevenson, W. F. Drew Bennett, Daniel A. Kirshner, Sergio E. 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) (2021)
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) (2021)
Derek Jones, Hyojin Kim, Xiaohua Zhang, Adam T. Zemla, Garrett Stevenson, William D. Bennett, Daniel A. Kirshner, Sergio E. Wong, Felice C. Lightstone, Jonathan E. Allen
Improved Protein-ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference. CoRR (2020)
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) (2020)
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) (2020)
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 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)
Timothy S. Carpenter, Felice C. Lightstone
An Electrostatic Funnel in the GABA-Binding Pathway. PLoS Comput. Biol. 12 (4) (2016)
Xiaohua Zhang, Horacio Pérez Sánchez, Felice C. Lightstone
Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach. IWBBIO (2) (2015)
Xiaohua Zhang, Sergio E. 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) (2014)
Xiaohua Zhang, Sergio E. 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) (2013)
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) (2013)