Search Results - "Koes, R"

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…”
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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…”
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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…”
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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…”
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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…”
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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…”
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Screening and In Vitro Testing of Antifolate Inhibitors of Human Cytosolic Serine Hydroxymethyltransferase by Paiardini, Alessandro, Fiascarelli, Alessio, Rinaldo, Serena, Daidone, Frederick, Giardina, Giorgio, Koes, David R., Parroni, Alessia, Montini, Giulia, Marani, Marina, Paone, Alessio, McDermott, Lee A., Contestabile, Roberto, Cutruzzolà, Francesca

“…Metabolic reprogramming of tumor cells toward serine catabolism is now recognized as a hallmark of cancer. Serine hydroxymethyltransferase (SHMT), the enzyme…”
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anthocyanin1 of Petunia Encodes a Basic Helix-Loop-Helix Protein That Directly Activates Transcription of Structural Anthocyanin Genes by Spelt, Cornelis, Quattrocchio, Francesca, Joseph N. M. Mol, Koes, Ronald

“…The petunia loci anthocyanin1 (an1), an2, an4, and an11 are required for the transcription of anthocyanin biosynthetic genes in floral organs. The an2 and an11…”
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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…”
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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…”
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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…”
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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…”
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The an11 locus controlling flower pigmentation in petunia encodes a novel WD-repeat protein conserved in yeast, plants, and animals by de Vetten, N, Quattrocchio, F, Mol, J, Koes, R

“…In petunia flowers, the loci an1, an2, and an11 control the pigmentation of the flower by stimulating the transcription of anthocyanin biosynthetic genes. The…”
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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…”
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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…”
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Correction to “SolTranNetA Machine Learning Tool for Fast Aqueous Solubility Prediction” by Francoeur, Paul G, Koes, David R

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Regulatory genes controlling anthocyanin pigmentation are functionally conserved among plant species and have distinct sets of target genes by QUATTROCCHIO, F, WING, J. F, LEPPEN, H. T. C, MOL, J. N. M, KOES, R. E

“…In this study, we demonstrate that in petunia at least four regulatory genes (anthocyanin-1 [an1], an2, an4, and an11) control transcription of a subset of…”
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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…”
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Selection of high-affinity phage antibodies from phage display libraries by Quattrocchio, Francesca, Bruin, Robert de, Spelt, Kees, Mol, Joseph, Koes, Ronald

“…Successful screening of phage display libraries will lead to more efficient, inexpensive antibody production…”
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Genetic control of branching pattern and floral identity during Petunia inflorescence development by Souer, E, van der Krol, A, Kloos, D, Spelt, C, Bliek, M, Mol, J, Koes, R

“…A main determinant of inflorescence architecture is the site where floral meristems are initiated. We show that in wild-type Petunia bifurcation of the…”
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