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ORCIDDavid Ryan Koes
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- affiliation: University of Pittsburgh, PA, USA
- affiliation (former): Carnegie Mellon University, Pittsburgh, USA
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2020 – today
- 2024
[j26]Andrew T. McNutt, David Ryan Koes:
Open-ComBind: harnessing unlabeled data for improved binding pose prediction. J. Comput. Aided Mol. Des. 38(1): 3 (2024)- [j25]Michael Brocidiacono
, Paul G. Francoeur, Rishal Aggarwal, Konstantin I. Popov, David Ryan Koes, Alexander Tropsha:
BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. J. Chem. Inf. Model. 64(7): 2488-2495 (2024) - [j24]Roshni Bhatt, David Ryan Koes, Jacob D. Durrant:
CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks. J. Chem. Inf. Model. 64(12): 4651-4660 (2024) - [j23]Fengling Li, Suzanne Ackloo, Cheryl H. Arrowsmith, Fuqiang Ban, Christopher J. Barden, Hartmut Beck, Jan Beránek, Francois Berenger, Albina Bolotokova, Guillaume Bret, Marko Breznik, Emanuele Carosati, Irene Chau, Yu Chen, Artem Cherkasov, Dennis Della Corte, Katrin Denzinger, Aiping Dong, Sorin Draga, Ian Dunn, Kristina Edfeldt, Aled M. Edwards, Merveille K. I. Eguida, Paul Eisenhuth, Lukas Friedrich, Alexander Fuerll, Spencer S. Gardiner, Francesco Gentile, Pegah Ghiabi, Elisa Gibson, Marta Glavatskikh, Christoph Gorgulla, Judith Guenther, Anders Gunnarsson, Filipp Gusev, Evgeny Gutkin, Levon Halabelian, Rachel J. Harding, Alexander Hillisch, Laurent Hoffer, Anders Hogner, Scott Houliston, John J. Irwin, Olexandr Isayev, Aleksandra Ivanova, Célien Jacquemard, Austin J. Jarrett, Jan H. Jensen, Dmitri Kireev, Julian Kleber, S. Benjamin Koby, David Koes, Ashutosh Kumar, Maria G. Kurnikova, Alina Kutlushina, Uta F. Lessel, Fabian Liessmann, Sijie Liu, Wei Lu, Jens Meiler, Akhila Mettu, Guzel Minibaeva, Rocco Moretti, Connor J. Morris, Chamali Narangoda, Theresa Noonan, Leon Obendorf, Szymon Pach, Amit Pandit, Sumera Perveen, Gennady Poda, Pavel G. Polishchuk, Kristina Puls, Vera Pütter, Didier Rognan, Dylan Roskams-Edris, Christina E. M. Schindler, François Sindt, Vojtech Spiwok, Casper Steinmann, Rick L. Stevens, Valerij Talagayev, Damon Tingey, Oanh Vu, W. Patrick Walters, Xiaowen Wang, Zhenyu Wang, Gerhard Wolber, Clemens Alexander Wolf, Lars Wortmann, Hong Zeng, Carlos A. Zepeda, Kam Y. J. Zhang, Jixian Zhang, Shuangjia Zheng, Matthieu Schapira:
CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. J. Chem. Inf. Model. 64(22): 8521-8536 (2024) - [i12]Ian Dunn, David Ryan Koes:
Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation. CoRR abs/2404.19739 (2024) - [i11]Andrew T. McNutt, Abhinav Adduri, Caleb N. Ellington, Monica T. Dayao, Eric P. Xing, Hosein Mohimani, David Ryan Koes:
SPRINT Enables Interpretable and Ultra-Fast Virtual Screening against Thousands of Proteomes. CoRR abs/2411.15418 (2024) - [i10]Ian Dunn, David Ryan Koes:
Exploring Discrete Flow Matching for 3D De Novo Molecule Generation. CoRR abs/2411.16644 (2024) - 2023
- [j22]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? J. Chem. Inf. Model. 63(21): 6598-6607 (2023) - [j21]Dakota L. Folmsbee, David Ryan Koes, Geoffrey R. Hutchison:
Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences. J. Chem. Inf. Model. 63(23): 7401-7411 (2023) - [i9]Ian Dunn, David Ryan Koes:
Accelerating Inference in Molecular Diffusion Models with Latent Representations of Protein Structure. CoRR abs/2311.13466 (2023) - 2022
- [j20]Andrew T. McNutt, David Ryan Koes:
Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network. J. Chem. Inf. Model. 62(8): 1819-1829 (2022) - 2021
- [j19]Andrew T. McNutt, Paul G. Francoeur, Rishal Aggarwal, Tomohide Masuda, Rocco Meli, Matthew Ragoza, Jocelyn Sunseri, David Ryan Koes:
GNINA 1.0: molecular docking with deep learning. J. Cheminformatics 13(1): 43 (2021) - [j18]Paul G. Francoeur, David Ryan Koes:
SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction. J. Chem. Inf. Model. 61(6): 2530-2536 (2021) - [j17]Paul G. Francoeur, David Ryan Koes:
Correction to "SolTranNet - A Machine Learning Tool for Fast Aqueous Solubility Prediction". J. Chem. Inf. Model. 61(8): 4120-4123 (2021) - [i8]Matthew Ragoza, Tomohide Masuda, David Ryan Koes:
Generating 3D Molecules Conditional on Receptor Binding Sites with Deep Generative Models. CoRR abs/2110.15200 (2021) - 2020
- [j16]Jocelyn Sunseri, David Ryan Koes:
libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications. J. Chem. Inf. Model. 60(3): 1079-1084 (2020) - [j15]Paul G. Francoeur, Tomohide Masuda, Jocelyn Sunseri, 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. J. Chem. Inf. Model. 60(9): 4200-4215 (2020) - [i7]Jonathan E. King, David Ryan Koes:
SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning. CoRR abs/2010.08162 (2020) - [i6]Matthew Ragoza, Tomohide Masuda, David Ryan Koes:
Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models. CoRR abs/2010.08687 (2020) - [i5]Tomohide Masuda, Matthew Ragoza, David Ryan Koes:
Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models. CoRR abs/2010.14442 (2020)
2010 – 2019
- 2019
- [j14]Jocelyn Sunseri, Jonathan E. King, Paul G. Francoeur, David Ryan Koes:
Convolutional neural network scoring and minimization in the D3R 2017 community challenge. J. Comput. Aided Mol. Des. 33(1): 19-34 (2019) - [i4]Jocelyn Sunseri, David Ryan Koes:
libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications. CoRR abs/1912.04822 (2019) - 2018
- [j13]David Ryan Koes:
The Pharmit backend: A computer systems approach to enabling interactive online drug discovery. IBM J. Res. Dev. 62(6): 3:1-3:6 (2018) - [i3]Joshua E. Hochuli, Alec Helbling, Tamar Skaist, Matthew Ragoza, David Ryan Koes:
Visualizing Convolutional Neural Network Protein-Ligand Scoring. CoRR abs/1803.02398 (2018) - 2017
- [j12]Matthew Ragoza, Joshua E. Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes:
Protein-Ligand Scoring with Convolutional Neural Networks. J. Chem. Inf. Model. 57(4): 942-957 (2017) - [i2]Matthew Ragoza, Lillian Turner, David Ryan Koes:
Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks. CoRR abs/1710.07400 (2017) - 2016
- [j11]Jocelyn Sunseri, Matthew Ragoza, Jasmine Collins, David Ryan Koes:
A D3R prospective evaluation of machine learning for protein-ligand scoring. J. Comput. Aided Mol. Des. 30(9): 761-771 (2016) - [j10]Jocelyn Sunseri, David Ryan Koes:
Pharmit: interactive exploration of chemical space. Nucleic Acids Res. 44(Webserver-Issue): W442-W448 (2016) - [i1]Matthew Ragoza, Joshua E. Hochuli, Elisa Idrobo, Jocelyn Sunseri, David Ryan Koes:
Protein-Ligand Scoring with Convolutional Neural Networks. CoRR abs/1612.02751 (2016) - 2015
- [j9]Nicholas Rego, David Koes:
3Dmol.js: molecular visualization with WebGL. Bioinform. 31(8): 1322-1324 (2015) - [j8]David Ryan Koes, Carlos J. Camacho:
Indexing volumetric shapes with matching and packing. Knowl. Inf. Syst. 43(1): 157-180 (2015) - 2014
- [j7]David Ryan Koes, Carlos J. Camacho:
Shape-based virtual screening with volumetric aligned molecular shapes. J. Comput. Chem. 35(25): 1824-1834 (2014) - 2013
- [j6]David Ryan Koes, Matthew P. Baumgartner, Carlos J. Camacho:
Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise. J. Chem. Inf. Model. 53(8): 1893-1904 (2013) - 2012
- [j5]David Ryan Koes, Carlos J. Camacho:
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinform. 28(6): 784-791 (2012) - [j4]David Ryan Koes, Carlos J. Camacho:
Small-molecule inhibitor starting points learned from protein-protein interaction inhibitor structure. Bioinform. 28(14): 1951 (2012) - [j3]David Ryan Koes, Carlos J. Camacho:
PocketQuery: protein-protein interaction inhibitor starting points from protein-protein interaction structure. Nucleic Acids Res. 40(Web-Server-Issue): 387-392 (2012) - [j2]David Ryan Koes, Carlos J. Camacho:
ZINCPharmer: pharmacophore search of the ZINC database. Nucleic Acids Res. 40(Web-Server-Issue): 409-414 (2012) - 2011
- [j1]David Ryan Koes, Carlos J. Camacho:
Pharmer: Efficient and Exact Pharmacophore Search. J. Chem. Inf. Model. 51(6): 1307-1314 (2011)
2000 – 2009
- 2009
- [c6]David Ryan Koes, Seth Copen Goldstein:
Register allocation deconstructed. SCOPES 2009: 21-30 - 2008
- [c5]David Ryan Koes, Seth Copen Goldstein:
Near-optimal instruction selection on dags. CGO 2008: 45-54 - 2006
- [c4]David Ryan Koes, Seth Copen Goldstein:
A global progressive register allocator. PLDI 2006: 204-215 - 2005
- [c3]David Koes, Seth Copen Goldstein:
A Progressive Register Allocator for Irregular Architectures. CGO 2005: 269-280 - 2004
- [c2]David Koes, Mihai Budiu, Girish Venkataramani:
Programmer specified pointer independence. Memory System Performance 2004: 51-59 - 2001
- [c1]Dennis Strelow, Jeffrey Mishler, David Koes, Sanjiv Singh:
Precise Omnidirectional Camera Calibration. CVPR (1) 2001: 689-694
Coauthor Index
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