Search Results - "Koes, David"

Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening by Chen, Lieyang, Cruz, Anthony, Ramsey, Steven, Dickson, Callum J, Duca, Jose S, Hornak, Viktor, Koes, David R, Kurtzman, Tom

“…Recently much effort has been invested in using convolutional neural network (CNN) models trained on 3D structural images of protein-ligand complexes to…”
Get full text

libmolgrid: Graphics Processing Unit Accelerated Molecular Gridding for Deep Learning Applications by Sunseri, Jocelyn, Koes, David R

“…We describe libmolgrid, a general-purpose library for representing three-dimensional molecules using multidimensional arrays of voxelized molecular data…”
Get full text

SolTranNet–A Machine Learning Tool for Fast Aqueous Solubility Prediction by Francoeur, Paul G, Koes, David R

“…While accurate prediction of aqueous solubility remains a challenge in drug discovery, machine learning (ML) approaches have become increasingly popular for…”
Get full text

DeepFrag: a deep convolutional neural network for fragment-based lead optimization by Green, Harrison, Koes, David R, Durrant, Jacob D

“…Machine learning has been increasingly applied to the field of computer-aided drug discovery in recent years, leading to notable advances in binding-affinity…”
Get full text

GNINA 1.0: molecular docking with deep learning by McNutt, Andrew T., Francoeur, Paul, Aggarwal, Rishal, Masuda, Tomohide, Meli, Rocco, Ragoza, Matthew, Sunseri, Jocelyn, Koes, David Ryan

“…Molecular docking computationally predicts the conformation of a small molecule when binding to a receptor. Scoring functions are a vital piece of any…”
Get full text

Improvements to the APBS biomolecular solvation software suite by 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.

“…The Adaptive Poisson–Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that…”
Get full text

Three-Dimensional Convolutional Neural Networks and a Cross-Docked Data Set for Structure-Based Drug Design by Francoeur, Paul G, Masuda, Tomohide, Sunseri, Jocelyn, Jia, Andrew, Iovanisci, Richard B, Snyder, Ian, Koes, David R

“…One of the main challenges in drug discovery is predicting protein–ligand binding affinity. Recently, machine learning approaches have made substantial…”
Get full text

Pharmit: interactive exploration of chemical space by Sunseri, Jocelyn, Koes, David Ryan

“…Pharmit (http://pharmit.csb.pitt.edu) provides an online, interactive environment for the virtual screening of large compound databases using pharmacophores,…”
Get full text

Generating 3D molecules conditional on receptor binding sites with deep generative models by Ragoza, Matthew, Masuda, Tomohide, Koes, David Ryan

“…The goal of structure-based drug discovery is to find small molecules that bind to a given target protein. Deep learning has been used to generate drug-like…”
Get full text

Deciphering the Role of Fatty Acid-Metabolizing CYP4F11 in Lung Cancer and Its Potential As a Drug Target by Jia, Huiting, Brixius, Bjoern, Bocianoski, Caleb, Ray, Sutapa, Koes, David R, Brixius-Anderko, Simone

“…Lung cancer is the leading cause of cancer deaths worldwide. We found that the cytochrome P450 isoform CYP4F11 is significantly overexpressed in patients with…”
Get full text

Systematic Comparison of Experimental Crystallographic Geometries and Gas-Phase Computed Conformers for Torsion Preferences by Folmsbee, Dakota L., Koes, David R., Hutchison, Geoffrey R.

“…We performed exhaustive torsion sampling on more than 3 million compounds using the GFN2-xTB method and performed a comparison of experimental crystallographic…”
Get full text

AnchorQuery: Rapid online virtual screening for small‐molecule protein–protein interaction inhibitors by Koes, David R., Dömling, Alexander, Camacho, Carlos J.

“…AnchorQuery (http://anchorquery.csb.pitt.edu) is a web application for rational structure‐based design of protein–protein interaction (PPI) inhibitors. A…”
Get full text

Evaluation of Thermochemical Machine Learning for Potential Energy Curves and Geometry Optimization by Folmsbee, Dakota L, Koes, David R, Hutchison, Geoffrey R

“…While many machine learning (ML) methods, particularly deep neural networks, have been trained for density functional and quantum chemical energies and…”
Get full text

Correction to “SolTranNetA Machine Learning Tool for Fast Aqueous Solubility Prediction” by Francoeur, Paul G, Koes, David R

Get full text

Virtual Screening with Gnina 1.0 by Sunseri, Jocelyn, Koes, David Ryan

“…Virtual screening-predicting which compounds within a specified compound library bind to a target molecule, typically a protein-is a fundamental task in the…”
Get full text

SidechainNet: An all‐atom protein structure dataset for machine learning by King, Jonathan Edward, Koes, David Ryan

“…Despite recent advancements in deep learning methods for protein structure prediction and representation, little focus has been directed at the simultaneous…”
Get full text

Evaluating amber force fields using computed NMR chemical shifts by Koes, David R., Vries, John K.

“…NMR chemical shifts can be computed from molecular dynamics (MD) simulations using a template matching approach and a library of conformers containing chemical…”
Get full text

Expanding Training Data for Structure-Based Receptor–Ligand Binding Affinity Regression through Imputation of Missing Labels by Francoeur, Paul G., Koes, David R.

“…The success of machine learning is, in part, due to a large volume of data available to train models. However, the amount of training data for structure-based…”
Get full text

Threonine 89 Is an Important Residue of Profilin-1 That Is Phosphorylatable by Protein Kinase A by Gau, David, Veon, William, Zeng, Xuemei, Yates, Nathan, Shroff, Sanjeev G, Koes, David R, Roy, Partha

“…Dynamic regulation of actin cytoskeleton is at the heart of all actin-based cellular events. In this study, we sought to identify novel post-translational…”
Get full text

Enabling large-scale design, synthesis and validation of small molecule protein-protein antagonists by Koes, David, Khoury, Kareem, Huang, Yijun, Wang, Wei, Bista, Michal, Popowicz, Grzegorz M, Wolf, Siglinde, Holak, Tad A, Dömling, Alexander, Camacho, Carlos J

“…Although there is no shortage of potential drug targets, there are only a handful known low-molecular-weight inhibitors of protein-protein interactions (PPIs)…”
Get full text