Wendy D. Cornell - researchr alias

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Viewing Publication 1 - 14 from 14

2024

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicityJeffrey K. Weber, Joseph A. Morrone, Seung Gu Kang, Leili Zhang, Lijun Lang, Diego Chowell, Chirag Krishna, Tien Huynh, Prerana Parthasarathy, Binquan Luan, Tyler J. Alban, Wendy D. Cornell, Timothy A Chan. bib, 25(Supplement 1), 2024. [doi]

2022

Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D ModelJannis Born, Tien Huynh, Astrid Stroobants, Wendy D. Cornell, Matteo Manica. jcisd, 62(2):240-257, 2022. [doi]

On the Choice of Active Site Sequences for Kinase-Ligand Affinity PredictionJannis Born, Yoel Shoshan, Tien Huynh, Wendy D. Cornell, Eric J. Martin, Matteo Manica. jcisd, 62(18):4295-4299, 2022. [doi]

Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational Autoencoder─Insights for Practical AI-Driven Molecule GenerationSeung Gu Kang, Joseph A. Morrone, Jeffrey K. Weber, Wendy D. Cornell. jcisd, 62(4):801-816, 2022. [doi]

Simplified, interpretable graph convolutional neural networks for small molecule activity predictionJeffrey K. Weber, Joseph A. Morrone, Sugato Bagchi, Jan D. Estrada Pabon, Seung Gu Kang, Leili Zhang, Wendy D. Cornell. jcamd, 36(5):391-404, 2022. [doi]

2020

Combining Docking Pose Rank and Structure with Deep Learning Improves Protein-Ligand Binding Mode Prediction over a Baseline Docking ApproachJoseph A. Morrone, Jeffrey K. Weber, Tien Huynh, Heng Luo 0002, Wendy D. Cornell. jcisd, 60(9):4170-4179, 2020. [doi]

2010

Drug-like Density: A Method of Quantifying the "Bindability" of a Protein Target Based on a Very Large Set of Pockets and Drug-like Ligands from the Protein Data BankRobert P. Sheridan, Vladimir N. Maiorov, M. Katharine Holloway, Wendy D. Cornell, Ying-Duo Gao. jcisd, 50(11):2029-2040, 2010. [doi]

2009

QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data SetsRobert P. Sheridan, Kiyean Nam, Vladimir N. Maiorov, Daniel R. McMasters, Wendy D. Cornell. jcisd, 49(8):1974-1985, 2009. [doi]

2008

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening resultsRobert P. Sheridan, Georgia B. McGaughey, Wendy D. Cornell. jcamd, 22(3-4):257-265, 2008. [doi]

2007

Comparison of Topological, Shape, and Docking Methods in Virtual ScreeningGeorgia B. McGaughey, Robert P. Sheridan, Christopher I. Bayly, J. Christopher Culberson, Constantine Kreatsoulas, Stacey Lindsley, Vladimir N. Maiorov, Jean-François Truchon, Wendy D. Cornell. jcisd, 47(4):1504-1519, 2007. [doi]

1996

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamicsWendy D. Cornell, Maria P. Ha, Yax Sun, Peter A. Kollman. jcc, 17(13):1541-1548, 1996. [doi]

1995

Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers: Charge Derication for DNA, RNA, and ProteinsPiotr Cieplak, Wendy D. Cornell, Christopher I. Bayly, Peter A. Kollman. jcc, 16(11):1357-1376, 1995.

Calculation of Molecular Geometries, Relative Conformational Energies, Dipole Moments, and Molecular Electrostatic Potential Fitted Charges of Small Organic Molecules of Biochemical Interest by Density Function TheoryAlain St.-Amant, Wendy D. Cornell, Peter A. Kollman, Thomas A. Halgren. jcc, 16(12):1483-1506, 1995.

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