Derek Jones

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Jonathan E AllenLawrence Livermore National LaboratoryVerified email at llnl.gov
Felice C. LightstoneSenior Scientist, Lawrence Livermore National LaboratoryVerified email at llnl.gov
W.F. Drew BennettLawrence Livermore National LabVerified email at llnl.gov
Xiaohua ZhangLawrence Livermore National LaboratoryVerified email at llnl.gov
Hyojin KimLawrence Livermore National LaboratoryVerified email at llnl.gov
Adam ZemlaComputer Scientist, LLNLVerified email at llnl.gov
Kevin S. McLoughlinLawrence Livermore National LaboratoryVerified email at llnl.gov
Sally R EllingsonAssistant ProfessorVerified email at uky.edu
Niema MoshiriAssociate Teaching Professor, University of California, San DiegoVerified email at ucsd.edu
Yue YangComputational Chemist, LLNLVerified email at llnl.gov
Camille BilodeauAssistant ProfessorVerified email at virginia.edu
Stewart HeData Scientist, Lawrence Livermore National LaboratoryVerified email at llnl.gov
Delin SunLawrence Livermore National LaboratoryVerified email at llnl.gov
Helgi I. IngólfssonLawrence Livermore National LaboratoryVerified email at llnl.gov
Jeevith BopaiahGraduate Student in Computer Science, University of KentuckyVerified email at uky.edu
Fatemah AlghamedyAssistant Prof.Verified email at iau.edu.sa
Ian KarlinLawrence Livermore National LaboratoryVerified email at colorado.edu
Dong H. AhnLLNLVerified email at llnl.gov
Brian Van EssenLawrence Livermore National LaboratoryVerified email at llnl.gov
Xiaofei ZhangUniversity of KentuckyVerified email at uky.edu

Derek Jones

Lawrence Livermore National Laboratory, University of California - San Diego

Verified email at llnl.gov - Homepage

Machine Learning Biophysics Drug Discovery High Performance Computing


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Improved Protein–Ligand Binding Affinity Prediction with Structure-Based Deep Fusion Inference D Jones, H Kim, X Zhang, A Zemla, G Stevenson, WFD Bennett, ... Journal of Chemical Information and Modeling 61 (4), 1583-1592, 2021	181	2021
Binding Affinity Prediction by Pairwise Function Based on Neural Network F Zhu, X Zhang, JE Allen, D Jones, FC Lightstone Journal of chemical information and modeling 60 (6), 2766-2772, 2020	47	2020
Predicting small molecule transfer free energies by combining molecular dynamics simulations and deep learning WFD Bennett, S He, CL Bilodeau, D Jones, D Sun, H Kim, JE Allen, ... Journal of Chemical Information and Modeling 60 (11), 5375-5381, 2020	44	2020
Enabling rapid COVID-19 small molecule drug design through scalable deep learning of generative models SA Jacobs, T Moon, K McLoughlin, D Jones, D Hysom, DH Ahn, ... The International Journal of High Performance Computing Applications 35 (5 …, 2021	32	2021
Accelerators for Classical Molecular Dynamics Simulations of Biomolecules D Jones, JE Allen, Y Yang, WF Drew Bennett, M Gokhale, N Moshiri, ... Journal of chemical theory and computation 18 (7), 4047-4069, 2022	24	2022
Discovery of small-molecule inhibitors of SARS-CoV-2 proteins using a computational and experimental pipeline EY Lau, OA Negrete, WFD Bennett, BJ Bennion, M Borucki, F Bourguet, ... Frontiers in Molecular Biosciences 8, 678701, 2021	22	2021
High-throughput virtual screening of small molecule inhibitors for sars-cov-2 protein targets with deep fusion models GA Stevenson, D Jones, H Kim, WFD Bennett, BJ Bennion, M Borucki, ... Proceedings of the International Conference for High Performance Computing …, 2021	12	2021
Incorporating protein dynamics through ensemble docking in machine learning models to predict drug binding F Alghamedy, J Bopaiah, D Jones, X Zhang, HL Weiss, SR Ellingson AMIA Summits on Translational Science Proceedings 2018, 26, 2018	12	2018
Polypharmacology within the full kinome: a machine learning approach D Jones, J Bopaiah, F Alghamedy, N Jacobs, HL Weiss, WA de Jong, ... AMIA Summits on Translational Science Proceedings 2018, 98, 2018	6	2018
Generative Molecular Design and Experimental Validation of Selective Histamine H1 Inhibitors KS McLoughlin, D Shi, JE Mast, J Bucci, JP Williams, WD Jones, D Miyao, ... bioRxiv, 2023.02. 14.528391, 2023	2	2023
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations D Jones, JE Allen, X Zhang, B Khaleghi, J Kang, W Xu, N Moshiri, ... arXiv preprint arXiv:2303.15604, 2023	1	2023
High-Throughput Virtual Screening of Small Molecule Inhibitors for SARS-CoV-2 Protein Targets with Deep Fusion Models (preprint) GA Stevenson, D Jones, H Kim, WFD Bennett, BJ Bennion, M Borucki, ...	1	2021
Advances in Computational Approaches for Estimating Passive Permeability in Drug Discovery A Bernardi, WFD Bennett, S He, D Jones, D Kirshner, BJ Bennion, ... Membranes 13 (11), 851, 2023		2023
Clustering Protein Binding Pockets and Identifying Potential Drug Interactions: A Novel Ligand-Based Featurization Method GA Stevenson, D Kirshner, BJ Bennion, Y Yang, X Zhang, A Zemla, ... Journal of Chemical Information and Modeling 63 (21), 6655-6666, 2023		2023
CAFCW 122 Fusion of Structure Based Deep Learning to Accelerate Molecular Docking Predictions D Jones		2019
Scalable Feature Selection and Extraction with Applications in Kinase Polypharmacology D Jones		2018
How Low Can You Go? Feature Selection for Drug Discovery D Jones, SR Ellingson, WA de Jong

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