Deep-learning: investigating deep neural networks hyper-parameters and comparison of performance to shallow methods for modeling bioactivity data

Alexios Koutsoukas, Keith J. Monaghan, Xiaoli Li, +1

Journal of Cheminformatics

In Silico Target Predictions: Defining a Benchmarking Data Set and Comparison of Performance of the Multiclass Naïve Bayes and Parzen-Rosenblatt Window

Alexios Koutsoukas, Robert Lowe, Yasaman KalantarMotamedi, +5

Journal of Chemical Information and Modeling

Benchmarking Data SetDrug TargetEngineeringMachine LearningHit Identification +27

How Diverse Are Diversity Assessment Methods? A Comparative Analysis and Benchmarking of Molecular Descriptor Space

Alexios Koutsoukas, Shardul Paricharak, Warren R. J. D. Galloway, +5

Journal of Chemical Information and Modeling

Hit IdentificationA Comparative AnalysisNatural DiversityRapid OverlayGenomics +26

AP-Net: An atomic-pairwise neural network for smooth and transferable interaction potentials

Zachary L. Glick, Derek P. Metcalf, Alexios Koutsoukas, +3

The Journal of Chemical Physics

Chemogenomics Approaches to Rationalizing the Mode-of-Action of Traditional Chinese and Ayurvedic Medicines

Fazlin Mohd Fauzi, Alexios Koutsoukas, Robert Lowe, +4

Journal of Chemical Information and Modeling

Traditional ChineseDrug TargetChemoprevention StrategyEducationMedicinal Chemistry +17

Approaches for machine learning intermolecular interaction energies and application to energy components from symmetry adapted perturbation theory

Derek P. Metcalf, Alexios Koutsoukas, Steven A. Spronk, +5

The Journal of Chemical Physics

CLIFF: A component-based, machine-learned, intermolecular force field

Jeffrey B. Schriber, Daniel R. Nascimento, Alexios Koutsoukas, +3

The Journal of Chemical Physics

Predictive Toxicology: Modeling Chemical Induced Toxicological Response Combining Circular Fingerprints with Random Forest and Support Vector Machine

Alexios Koutsoukas, Joseph St. Amand, Meenakshi Mishra, +1

Frontiers in Environmental Science

EngineeringToxicology TestingMedicinal ChemistrySupport Vector MachineData Science +24

Anti-cancer Drug Development: Computational Strategies to Identify and Target Proteins Involved in Cancer Metabolism

Lora Mak, Sonia Liggi, Lu Tan, +5

Current Pharmaceutical Design

Anti-cancer Drug DevelopmentComputational StrategiesEngineeringDrug TargetTumor Biology +20

Cartesian message passing neural networks for directional properties: Fast and transferable atomic multipoles

Zachary L. Glick, Alexios Koutsoukas, Daniel L. Cheney, +1

The Journal of Chemical Physics

EngineeringNeural NetworkComputational ChemistryChemistryMolecular Dynamics +22