David Ryan Koes

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A Better Global Progressive Register Allocator

David Ryan Koes, Seth Copen Goldstein, 2006 .

3D Convolutional Neural Networks and a CrossDocked Dataset for Structure-Based Drug Design.

David Ryan Koes, Paul Francoeur, Tomohide Masuda, 2020, Journal of chemical information and modeling.

Convolutional neural network scoring and minimization in the D3R 2017 community challenge

David Ryan Koes, Jocelyn Sunseri, Jonathan E. King, 2018, Journal of Computer-Aided Molecular Design.

Shape‐based virtual screening with volumetric aligned molecular shapes

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2014, J. Comput. Chem..

Generating 3D Molecular Structures Conditional on a Receptor Binding Site with Deep Generative Models pdf

David Ryan Koes, Tomohide Masuda, Matthew Ragoza, 2020, ArXiv.

Visualizing Convolutional Neural Network Protein-Ligand Scoring

David Ryan Koes, Joshua Hochuli, Matthew Ragoza, 2018, Journal of molecular graphics & modelling.

Pharmacophore Modeling: Methods and Applications

David Ryan Koes, D. Koes, 2015 .

Fragment oriented molecular shapes.

David Ryan Koes, Carlos J Camacho, Ethan Hain, 2016, Journal of molecular graphics & modelling.

Precise omnidirectional camera calibration

David Ryan Koes, Sanjiv Singh, Dennis Strelow, 2001, Proceedings of the 2001 IEEE Computer Society Conference on Computer Vision and Pattern Recognition. CVPR 2001.

Protein-Ligand Scoring with Convolutional Neural Networks

David Ryan Koes, Jocelyn Sunseri, Joshua Hochuli, 2016, Journal of chemical information and modeling.

A D3R prospective evaluation of machine learning for protein-ligand scoring

David Ryan Koes, Jocelyn Sunseri, Jasmine Collins, 2016, Journal of Computer-Aided Molecular Design.

An Analysis of Graph Coloring Register Allocation

David Ryan Koes, Seth Copen Goldstein, S. Goldstein, 2006 .

PocketQuery: protein–protein interaction inhibitor starting points from protein–protein interaction structure

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2012, Nucleic Acids Res..

A global progressive register allocator

David Ryan Koes, Seth Copen Goldstein, S. Goldstein, 2006, PLDI '06.

Pharmer: Efficient and Exact Pharmacophore Search

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2011, J. Chem. Inf. Model..

A progressive register allocator for irregular architectures

David Ryan Koes, Seth Copen Goldstein, S. Goldstein, 2005, International Symposium on Code Generation and Optimization.

ANCHOR.QUERY: A pharmacophore-based interactive screening technology for the discovery of potent and selective MDM2/p53 antagonist

David Ryan Koes, Grzegorz M. Popowicz, Carlos J. Camacho, 2013 .

Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2011, Bioinform..

Towards a more principled compiler: register allocation and instruction selection revisited

David Ryan Koes, Seth Copen Goldstein, S. Goldstein, 2009 .

The 3Dmol.js learning environment: a classroom response system for 3D chemical structures.

David Ryan Koes, Keshavan Seshadri, Peng Liu, 2020, Journal of chemical education.

Near-optimal instruction selection on dags

David Ryan Koes, Seth Copen Goldstein, 2008, CGO '08.

Adding Faster with Application Specific Early Termination

David Ryan Koes, Seth Copen Goldstein, Tiberiu Chelcea, 2005 .

Ligand Pose Optimization with Atomic Grid-Based Convolutional Neural Networks pdf

David Ryan Koes, Matthew Ragoza, Lillian Turner, 2017, ArXiv.

The Pharmit backend: A computer systems approach to enabling interactive online drug discovery

David Ryan Koes, D. Koes, 2018, IBM J. Res. Dev..

libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

David Ryan Koes, Jocelyn Sunseri, D. Koes, 2019, Journal of chemical information and modeling.

Programmer specified pointer independence

David Ryan Koes, Mihai Budiu, Girish Venkataramani, 2004, MSP '04.

Lessons Learned in Empirical Scoring with smina from the CSAR 2011 Benchmarking Exercise

David Ryan Koes, Carlos J. Camacho, Matthew P. Baumgartner, 2013, J. Chem. Inf. Model..

A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool

David Ryan Koes, Carlos J. Camacho, Margaret A. Phillips, 2015, PloS one.

Indexing volumetric shapes with matching and packing

David Ryan Koes, Carlos J. Camacho, 2014, Knowledge and Information Systems.

Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2011, Bioinform..

Open source molecular modeling.

David Ryan Koes, Jocelyn Sunseri, Somayeh Pirhadi, 2016, Journal of molecular graphics & modelling.

Learning a Continuous Representation of 3D Molecular Structures with Deep Generative Models pdf

David Ryan Koes, Tomohide Masuda, Matthew Ragoza, 2020, ArXiv.

David Ryan Koes, Seth Copen Goldstein, S. Goldstein, 2009, SCOPES.

Thesis Proposal Towards a More Principled Compiler: Progressive Backend Compiler Optimization

David Ryan Koes, D. Koes, 2006 .

SidechainNet: An All-Atom Protein Structure Dataset for Machine Learning pdf

David Ryan Koes, Jonathan E. King, 2020, ArXiv.

Pharmit: interactive exploration of chemical space

David Ryan Koes, Jocelyn Sunseri, D. Koes, 2016, Nucleic Acids Res..

ZINCPharmer: pharmacophore search of the ZINC database

David Ryan Koes, Carlos J. Camacho, C. Camacho, 2012, Nucleic Acids Res..

GNINA 1.0: molecular docking with deep learning

David Ryan Koes, Paul Francoeur, Tomohide Masuda, 2021, Journal of Cheminformatics.

Correction to "SolTranNet - A Machine Learning Tool for Fast Aqueous Solubility Prediction"

David Ryan Koes, Paul G. Francoeur, 2021, J. Chem. Inf. Model..

SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction

David Ryan Koes, Paul G. Francoeur, D. Koes, 2021, J. Chem. Inf. Model..

Generating 3D molecules conditional on receptor binding sites with deep generative models pdf

David Ryan Koes, Tomohide Masuda, Matthew Ragoza, 2021, Chemical science.

David Ryan Koes, 2009 .