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Comparison of Topological, Shape, and Docking Methods in Virtual Screening

Journal of chemical information and modeling, 2007-07, Vol.47 (4), p.1504-1519

2007

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Combining Docking Pose Rank and Structure with Deep Learning Improves Protein–Ligand Binding Mode Prediction over a Baseline Docking Approach

Journal of chemical information and modeling, 2020-09, Vol.60 (9), p.4170-4179

2020

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Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model

Journal of chemical information and modeling, 2022-01, Vol.62 (2), p.240-257

2022

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On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction

Journal of chemical information and modeling, 2022-09, Vol.62 (18), p.4295-4299

2022

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Journal of the American Chemical Society, 1995-05, Vol.117 (19), p.5179-5197

1995

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Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational AutoencoderInsights for Practical AI-Driven Molecule Generation

Journal of chemical information and modeling, 2022-02, Vol.62 (4), p.801-816

2022

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QSAR Prediction of Passive Permeability in the LLC-PK1 Cell Line: Trends in Molecular Properties and Cross-Prediction of Caco-2 Permeabilities

Molecular informatics, 2012-04, Vol.31 (3-4), p.231-245

2012

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Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation

Journal of the American Chemical Society, 1993-10, Vol.115 (21), p.9620-9631

1993

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Simplified, interpretable graph convolutional neural networks for small molecule activity prediction

Journal of computer-aided molecular design, 2022-05, Vol.36 (5), p.391-404

2022

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Inhibitors of Human Histone Deacetylase: Synthesis and Enzyme and Cellular Activity of Straight Chain Hydroxamates

Journal of medicinal chemistry, 2002-02, Vol.45 (4), p.753-757

2002

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Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity

Briefings in bioinformatics, 2024-01, Vol.25 (1)

2024

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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 Bank

Journal of chemical information and modeling, 2010-11, Vol.50 (11), p.2029-2040

2010

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Developing timely insights into comparative effectiveness research with a text-mining pipeline

Drug discovery today, 2016-03, Vol.21 (3), p.473-480

2016

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Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development

Drug discovery today, 2016-05, Vol.21 (5), p.826-835

2016

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Role of chronic toxicology studies in revealing new toxicities

Regulatory toxicology and pharmacology, 2016-12, Vol.82, p.94-98

2016

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A quantum Mechanical Investigation of the Conformational Energetics of the Alanine and Glycine Dipeptides in the Gas Phase and in Aqueous Solution

Journal of the American Chemical Society, 1994-10, Vol.116 (20), p.9250-9256

1994

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Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

Journal of computer-aided molecular design, 2008-03, Vol.22 (3-4), p.257-265

2008

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QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets

Journal of Chemical Information and Modeling, 2009-08, Vol.49 (8), p.1974-1985

2009

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Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins

Journal of computational chemistry, 1995-11, Vol.16 (11), p.1357-1377

1995

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

Journal of the American Chemical Society, 1996-03, Vol.118 (9), p.2309-2309

1996

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Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding – Consensus and Caveats

Annual Reports in Computational Chemistry, 2006, Vol.2, p.297-323

Cornell, Wendy D.

2006

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Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory

Journal of computational chemistry, 1995-12, Vol.16 (12), p.1483-1506

1995

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Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics

Journal of computational chemistry, 1996-10, Vol.17 (13), p.1541-1548

1996

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Molecular mechanical potential functions and their application to study molecular systems

Current opinion in structural biology, 1991-04, Vol.1 (2), p.201-212

1991

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Comparison of Topological, Shape, and Docking Methods in Virtual Screening

Combining Docking Pose Rank and Structure with Deep Learning Improves Protein–Ligand Binding Mode Prediction over a Baseline Docking Approach

Active Site Sequence Representations of Human Kinases Outperform Full Sequence Representations for Affinity Prediction and Inhibitor Generation: 3D Effects in a 1D Model

On the Choice of Active Site Sequences for Kinase-Ligand Affinity Prediction

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

Analysis of Training and Seed Bias in Small Molecules Generated with a Conditional Graph-Based Variational AutoencoderInsights for Practical AI-Driven Molecule Generation

QSAR Prediction of Passive Permeability in the LLC-PK1 Cell Line: Trends in Molecular Properties and Cross-Prediction of Caco-2 Permeabilities

Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation

Simplified, interpretable graph convolutional neural networks for small molecule activity prediction

Inhibitors of Human Histone Deacetylase: Synthesis and Enzyme and Cellular Activity of Straight Chain Hydroxamates

Unsupervised and supervised AI on molecular dynamics simulations reveals complex characteristics of HLA-A2-peptide immunogenicity

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 Bank

Developing timely insights into comparative effectiveness research with a text-mining pipeline

Application of an automated natural language processing (NLP) workflow to enable federated search of external biomedical content in drug discovery and development

Role of chronic toxicology studies in revealing new toxicities

A quantum Mechanical Investigation of the Conformational Energetics of the Alanine and Glycine Dipeptides in the Gas Phase and in Aqueous Solution

Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results

QSAR Models for Predicting the Similarity in Binding Profiles for Pairs of Protein Kinases and the Variation of Models between Experimental Data Sets

Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins

Discovery of Potent, Selective, and Orally Active Carboxylic Acid Based Inhibitors of Matrix Metalloproteinase-13

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

Chapter 16 Recent Evaluations of High Throughput Docking Methods for Pharmaceutical Lead Finding – Consensus and Caveats

Calculation of molecular geometries, relative conformational energies, dipole moments, and molecular electrostatic potential fitted charges of small organic molecules of biochemical interest by density functional theory

Application of a simple diagonal force field to the simulation of cyclopentane conformational dynamics

Molecular mechanical potential functions and their application to study molecular systems

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