Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening
Chen, Lieyang, Cruz, Anthony, Ramsey, Steven, Dickson, Callum J, Duca, Jose S, Hornak, Viktor, Koes, David R, Kurtzman, Tom
Published in PloS one (20.08.2019)
Published in PloS one (20.08.2019)
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Improvements to the APBS biomolecular solvation software suite
Jurrus, Elizabeth, Engel, Dave, Star, Keith, Monson, Kyle, Brandi, Juan, Felberg, Lisa E., Brookes, David H., Wilson, Leighton, Chen, Jiahui, Liles, Karina, Chun, Minju, Li, Peter, Gohara, David W., Dolinsky, Todd, Konecny, Robert, Koes, David R., Nielsen, Jens Erik, Head‐Gordon, Teresa, Geng, Weihua, Krasny, Robert, Wei, Guo‐Wei, Holst, Michael J., McCammon, J. Andrew, Baker, Nathan A.
Published in Protein science (01.01.2018)
Published in Protein science (01.01.2018)
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Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design
Francoeur, Paul G, Masuda, Tomohide, Sunseri, Jocelyn, Jia, Andrew, Iovanisci, Richard B, Snyder, Ian, Koes, David R
Published in Journal of chemical information and modeling (28.09.2020)
Published in Journal of chemical information and modeling (28.09.2020)
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Journal Article
Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A
Gau, David, Veon, William, Zeng, Xuemei, Yates, Nathan, Shroff, Sanjeev G, Koes, David R, Roy, Partha
Published in PloS one (26.05.2016)
Published in PloS one (26.05.2016)
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Journal Article
Screening and In Vitro Testing of Antifolate Inhibitors of Human Cytosolic Serine Hydroxymethyltransferase
Paiardini, Alessandro, Fiascarelli, Alessio, Rinaldo, Serena, Daidone, Frederick, Giardina, Giorgio, Koes, David R., Parroni, Alessia, Montini, Giulia, Marani, Marina, Paone, Alessio, McDermott, Lee A., Contestabile, Roberto, Cutruzzolà, Francesca
Published in ChemMedChem (01.03.2015)
Published in ChemMedChem (01.03.2015)
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libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications
Sunseri, Jocelyn, Koes, David R
Published in Journal of chemical information and modeling (23.03.2020)
Published in Journal of chemical information and modeling (23.03.2020)
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Journal Article
SolTranNet–A Machine Learning Tool for Fast Aqueous Solubility Prediction
Francoeur, Paul G, Koes, David R
Published in Journal of chemical information and modeling (28.06.2021)
Published in Journal of chemical information and modeling (28.06.2021)
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Journal Article
DeepFrag: a deep convolutional neural network for fragment-based lead optimization
Green, Harrison, Koes, David R, Durrant, Jacob D
Published in Chemical science (Cambridge) (08.05.2021)
Published in Chemical science (Cambridge) (08.05.2021)
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Journal Article
Correction to “SolTranNetA Machine Learning Tool for Fast Aqueous Solubility Prediction”
Francoeur, Paul G, Koes, David R
Published in Journal of chemical information and modeling (23.08.2021)
Published in Journal of chemical information and modeling (23.08.2021)
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Journal Article
Evaluation of Thermochemical Machine Learning for Potential Energy Curves and Geometry Optimization
Folmsbee, Dakota L, Koes, David R, Hutchison, Geoffrey R
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (11.03.2021)
Published in The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory (11.03.2021)
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Journal Article
Evaluating amber force fields using computed NMR chemical shifts
Koes, David R., Vries, John K.
Published in Proteins, structure, function, and bioinformatics (01.10.2017)
Published in Proteins, structure, function, and bioinformatics (01.10.2017)
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Journal Article
Selection of high-affinity phage antibodies from phage display libraries
Quattrocchio, Francesca, Bruin, Robert de, Spelt, Kees, Mol, Joseph, Koes, Ronald
Published in Nature biotechnology (01.04.1999)
Published in Nature biotechnology (01.04.1999)
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Journal Article
Genetic control of branching pattern and floral identity during Petunia inflorescence development
Souer, E, van der Krol, A, Kloos, D, Spelt, C, Bliek, M, Mol, J, Koes, R
Published in Development (Cambridge) (01.02.1998)
Published in Development (Cambridge) (01.02.1998)
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