David Ryan Koes (David R Koes)

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 28

Top Topics

Molecular Docking

Convolutional Neural Network

Machine Learning

Capillary Electrophoresis

Top Venues

Journal of chemical information and modeling

Journal of cheminformatics

Nucleic acids research

This page only lists publications with an associated author ORCID identifier.

Publications

Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Journal of chemical information and modeling 64 (12) (2024)
Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Journal of chemical information and modeling (2024)
Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Journal of chemical information and modeling 64 (12) (2024)
Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Journal of chemical information and modeling 64 (12) (2024)
Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. Journal of chemical information and modeling (2024)
Paul G Francoeur, David Ryan Koes
Expanding Training Data for Structure-Based Receptor-Ligand Binding Affinity Regression through Imputation of Missing Labels. ACS omega 8 (44) (2023)
Michael Brocidiacono, Paul G Francoeur, Rishal Aggarwal, Konstantin I Popov, David Ryan Koes, Alexander Trospsha
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. Journal of chemical information and modeling (2023)
Michael Brocidiacono, Paul G Francoeur, Rishal Aggarwal, Konstantin I Popov, David Ryan Koes, Alexander Trospsha
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. Journal of chemical information and modeling 64 (7) (2023)
Roshni Bhatt, David Ryan Koes, Jacob D Durrant
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. bioRxiv : the preprint server for biology (2023)
Michael Brocidiacono, Paul G Francoeur, Rishal Aggarwal, Konstantin I Popov, David Ryan Koes, Alexander Trospsha
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. Journal of chemical information and modeling (2023)
Andrew T McNutt, Fatimah Bisiriyu, Sophia Song, Ananya Vyas, Geoffrey R Hutchison, David Ryan Koes
Conformer Generation for Structure-Based Drug Design: How Many and How Good? Journal of chemical information and modeling (2023)
Michael Brocidiacono, Paul G Francoeur, Rishal Aggarwal, Konstantin I Popov, David Ryan Koes, Alexander Trospsha
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. Journal of chemical information and modeling 64 (7) (2023)
Michael Brocidiacono, Paul G Francoeur, Rishal Aggarwal, Konstantin I Popov, David Ryan Koes, Alexander Trospsha
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. Journal of chemical information and modeling 64 (7) (2023)
Dakota L Folmsbee, David Ryan Koes, Geoffrey R Hutchison
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. Journal of chemical information and modeling (2023)
Andrew T McNutt, David Ryan Koes
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. Journal of chemical information and modeling 62 (8) (2022)
Dakota L Folmsbee, David Ryan Koes, Geoffrey R Hutchison
Evaluation of Thermochemical Machine Learning for Potential Energy Curves and Geometry Optimization. The journal of physical chemistry. A 125 (9) (2021)
Paul G Francoeur, David Ryan Koes
SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction. Journal of chemical information and modeling 61 (6) (2021)
Andrew T McNutt, Paul Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, David Ryan Koes
GNINA 1.0: molecular docking with deep learning. Journal of cheminformatics 13 (1) (2021)
Paul G Francoeur, David Ryan Koes
Correction to "SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction". Journal of chemical information and modeling 61 (8) (2021)
Jonathan Edward King, David Ryan Koes
SidechainNet: An all-atom protein structure dataset for machine learning. Proteins 89 (11) (2021)
David Ryan Koes, David Ryan Koes
Virtual Screening with Gnina 1.0. Molecules (Basel, Switzerland) 26 (23) (2021)
Paul G Francoeur, Tomohide Masuda, David Ryan Koes, Andrew Jia, Richard B Iovanisci, Ian Snyder, David Ryan Koes
Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design. Journal of chemical information and modeling 60 (9) (2020)
David Ryan Koes, David Ryan Koes
libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. Journal of chemical information and modeling 60 (3) (2020)
David Ryan Koes, John K Vries
Evaluating amber force fields using computed NMR chemical shifts. Proteins 85 (10) (2017)
Matthew Ragoza, Joshua Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes
Protein-Ligand Scoring with Convolutional Neural Networks. Journal of chemical information and modeling 57 (4) (2017)
Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E Felberg, David H Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li, David W Gohara, Todd Dolinsky, Robert Konecny, David Ryan Koes, Jens Erik Nielsen, Teresa Head-Gordon, Weihua Geng, Robert Krasny, Guo-Wei Wei, Michael J Holst, J Andrew McCammon, Nathan A Baker
Improvements to the APBS biomolecular solvation software suite. Protein science : a publication of the Protein Society 27 (1) (2017)
David Ryan Koes, David Ryan Koes
Pharmit: interactive exploration of chemical space. Nucleic acids research 44 (W1) (2016)
Jocelyn Sunseri, Matthew Ragoza, Jasmine Collins, David Ryan Koes
A D3R prospective evaluation of machine learning for protein-ligand scoring. Journal of computer-aided molecular design 30 (9) (2016)