D. Koes

发表

A global progressive register allocator

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

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening

Viktor Hornak, David R Koes, Tom Kurtzman, 2019, PloS one.

Enabling Large-Scale Design, Synthesis and Validation of Small Molecule Protein-Protein Antagonists

Grzegorz M. Popowicz, Alexander Dömling, Carlos J. Camacho, 2012, PloS one.

Interactive Technologies for Leveraging the Known Chemistry of Anchor Residues to Disrupt Protein Interactions

C. Camacho, A. Dömling, D. Koes, 2013 .

Virtual-screening workflow tutorials and prospective results

Matthew P. Baumgartner, D. Koes, Andrea Volkamer, 2017 .

Build Simplify Potential Spill Select Actual Spill Coloring Heuristic

S. Goldstein, D. Koes, 2005 .

Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A

S. Shroff, D. Koes, N. Yates, 2016, PloS one.

Structure-based virtual screening identifies a small-molecule inhibitor of the profilin 1–actin interaction

P. Wipf, D. Koes, P. Roy, 2017, The Journal of Biological Chemistry.

Inhibition of ocular neovascularization by novel anti-angiogenic compound.

Paul G. Francoeur, X. Guillonneau, D. Koes, 2021, Experimental eye research.

Disruption of profilin1 function suppresses developmental and pathological retinal neovascularization

David N. Boone, J. Sahel, X. Guillonneau, 2020, The Journal of Biological Chemistry.

Structure Guided Chemical Modifications of Propylthiouracil Reveal Novel Small Molecule Inhibitors of Cytochrome b5 Reductase 3 That Increase Nitric Oxide Bioavailability*

Megan P. Miller, Bill B. Chen, C. Camacho, 2015, The Journal of Biological Chemistry.

NADPH oxidase 2 inhibitors CPP11G and CPP11H attenuate endothelial cell inflammation & vessel dysfunction and restore mouse hind-limb flow

C. Camacho, D. Koes, C. S. St. Croix, 2019, Redox biology.

Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network

Andrew T. McNutt, D. Koes, Andrew McNutt, 2021, J. Chem. Inf. Model..

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..

Indexing volumetric shapes with matching and packing

C. Camacho, D. Koes, 2015, Knowledge and Information Systems.

DeepFrag: a deep convolutional neural network for fragment-based lead optimization

Jacob D. Durrant, D. Koes, Harrison Green, 2021, bioRxiv.

Proposal : Register Allocation for Irregular Architectures

D. Koes, 2004 .

Exhaustive Fluorine Scanning toward Potent p53–Mdm2 Antagonists

T. Holak, C. Camacho, A. Dömling, 2012, ChemMedChem.

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..

Improvements to the APBS biomolecular solvation software suite

Jiahui Chen, Guo-Wei Wei, Nathan A. Baker, 2017, Protein science : a publication of the Protein Society.

A pyrazolopyran derivative preferentially inhibits the activity of human cytosolic serine hydroxymethyltransferase and induces cell death in lung cancer cells

Tianyi Yang, D. Koes, A. Paiardini, 2015, Oncotarget.

Screening and In Vitro Testing of Antifolate Inhibitors of Human Cytosolic Serine Hydroxymethyltransferase

D. Koes, A. Paiardini, F. Cutruzzolà, 2015, ChemMedChem.

Pharmer: Efficient and Exact Pharmacophore Search

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

3Dmol.js: molecular visualization with WebGL

Nicholas B Rego, D. Koes, 2014, Bioinform..

GNINA 1.0: molecular docking with deep learning

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

Protein-Ligand Scoring with Convolutional Neural Networks

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

SidechainNet: An all‐atom protein structure dataset for machine learning

D. Koes, J. E. King, J. E. King, 2020, Proteins.

Pharmit: interactive exploration of chemical space

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

GAC inhibitors with a 4-hydroxypiperidine spacer: Requirements for potency.

William P. Katt, D. Koes, R. Cerione, 2019, Bioorganic & medicinal chemistry letters.

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

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

Virtual Screening with Gnina 1.0

D. Koes, Jocelyn Sunseri, 2021, Molecules.

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.

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.

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

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

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.

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

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

Open source molecular modeling.

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

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

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

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

David Ryan Koes, D. Koes, 2006 .

ZINCPharmer: pharmacophore search of the ZINC database

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

Title Page In Silico Simulation of DUSP-YIV906 Protein-Ligand Interactions and DUSP3- ERK Protein-Peptide Interactions by

Lirong Wang, X. Xie, D. Koes, 2020 .

libmolgrid: GPU Accelerated Molecular Gridding for Deep Learning Applications

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

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.

AnchorQuery: Rapid online virtual screening for small‐molecule protein–protein interaction inhibitors

Alexander Dömling, David R. Koes, Carlos J. Camacho, 2018, Protein science : a publication of the Protein Society.

Actin-binding protein profilin1 promotes aggressiveness of clear-cell renal cell carcinoma cells

Paul G. Francoeur, J. Maranchie, M. Lotze, 2020, The Journal of Biological Chemistry.

A progressive register allocator for irregular architectures

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

Shape‐based virtual screening with volumetric aligned molecular shapes

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

Evaluation of Thermochemical Machine Learning for Potential Energy Curves and Geometry Optimization.

D Folmsbee, Koes Dr, G Hutchison, 2020, The journal of physical chemistry. A.

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

D. Koes, T. Masuda, Matthew Ragoza, 2020, ArXiv.

Finding Motifs in Protein-Protein Interaction Networks

Zhenzhen Kou, Juchang Hua, David Koes, 2003 .

Improving ΔΔG Predictions with a Multitask Convolutional Siamese Network

Andrew T McNutt, D. Koes, 2022, J. Chem. Inf. Model..

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

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

Assessing acquired resistance to IDH1 inhibitor therapy by full-exon IDH1 sequencing and structural modeling

Z. Oltvai, P. Mróz, D. Koes, 2021, Cold Spring Harbor molecular case studies.

Fragment oriented molecular shapes.

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

Characterization of Profilin Binding Kinetics using Ensemble Molecular Dynamics Simulations

D. Koes, P. Roy, D. Gau, 2017 .

Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design

Paul G. Francoeur, D. Koes, Jocelyn Sunseri, 2020, J. Chem. Inf. Model..

Pharmacophore Modeling: Methods and Applications

David Ryan Koes, D. Koes, 2015 .

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

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

NADPH oxidase 2 inhibitors CPP11G and CPP11H attenuate endothelial cell inflammation & vessel dysfunction and restore mouse hind-limb flow

Daniel N. Meijles, C. Camacho, D. Koes, 2019, Redox biology.

An Analysis of Graph Coloring Register Allocation

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

Register allocation deconstructed

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

PLANTAIN: Diffusion-inspired Pose Score Minimization for Fast and Accurate Molecular Docking

A. Tropsha, D. Koes, Konstantin I. Popov, 2023, ArXiv.

Error assessment in molecular dynamics trajectories using computed NMR chemical shifts.

D. Koes, J. K. Vries, 2017, Computational & theoretical chemistry.

Fragment oriented molecular shapes.

C. Camacho, D. Koes, Ethan Hain, 2016, Journal of Molecular Graphics and Modelling.

SolTranNet-A Machine Learning Tool for Fast Aqueous Solubility Prediction

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

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

Paul G. Francoeur, D. Koes, Tomohide Masuda, 2020 .

Protein-Ligand Scoring with Convolutional Neural Networks

D. Koes, Matthew Ragoza, Jocelyn Sunseri, 2017, J. Chem. Inf. Model..

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences

G. Hutchison, D. Koes, Dakota L Folmsbee, 2023, J. Chem. Inf. Model..

Conformer Generation for Structure-Based Drug Design: How Many and How Good?

Andrew T. McNutt, G. Hutchison, D. Koes, 2023, J. Chem. Inf. Model..

Virtual Screening with Gnina 1.0

D. Koes, Jocelyn Sunseri, 2021, Molecules.

Programmer specified pointer independence

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

FixingTIM: interactive exploration of sequence and structural data to identify functional mutations in protein families

Timothy Travers, John E. Wenskovitch, Timothy Luciani, 2014, BMC Proceedings.

BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening

Paul G. Francoeur, D. Koes, Rishal Aggarwal, 2023, J. Chem. Inf. Model..

CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks

D. Koes, Roshni Bhatt, Jacob D Durrant, 2023, bioRxiv.

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

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

Open-ComBind: harnessing unlabeled data for improved binding pose prediction

Andrew T. McNutt, D. Koes, 2023, Journal of Computer-Aided Molecular Design.

Visualizing Convolutional Neural Network Protein-Ligand Scoring

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

Mixed Continuous and Categorical Flow Matching for 3D De Novo Molecule Generation

D. Koes, Ian Dunn, 2024, ArXiv.

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.

CENsible: Interpretable Insights into Small-Molecule Binding with Context Explanation Networks

D. Koes, Jacob D Durrant, Roshni Bhatt, 2024, J. Chem. Inf. Model..

Structure-based virtual screening identifies a small-molecule inhibitor of the profilin 1–actin interaction

P. Wipf, D. Koes, P. Roy, 2017, The Journal of Biological Chemistry.

MOLUCINATE: A Generative Model for Molecules in 3D Space

D. Koes, Michael J. Arcidiacono, 2021, 2109.15308.

Actin-binding protein profilin1 is an important determinant of cellular phosphoinositide control

D. Koes, Gerald R. V. Hammond, Rachel C. Wills, 2023, The Journal of biological chemistry.

Deciphering the Role of Fatty Acid–Metabolizing CYP4F11 in Lung Cancer and Its Potential As a Drug Target

D. Koes, Sutapa Ray, H. Jia, 2023, Drug Metabolism and Disposition.