Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening

Lieyang Chen, Anthony Cruz, Steven Ramsey, +5

PLoS ONE

Artificial IntelligenceGeometric LearningConvolutional Neural NetworkEngineeringMachine Learning +16

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

Steven Ramsey, Crystal N. Nguyen, Romelia Salomón–Ferrer, +3

Journal of Computational Chemistry

A Novel Mitragynine Analog with Low-Efficacy Mu Opioid Receptor Agonism Displays Antinociception with Attenuated Adverse Effects

Soumen Chakraborty, Jeffrey F. DiBerto, Abdelfattah Faouzi, +21

Journal of Medicinal Chemistry

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories

Kamran Haider, Anthony Cruz, Steven Ramsey, +2

Journal of Chemical Theory and Computation

EngineeringFlexible PackageMolecular BiologyMolecular Dynamics TrajectoriesComputational Chemistry +16

Hidden Bias in the DUD-E Dataset Leads to Misleading Performance of Deep Learning in Structure-Based Virtual Screening

Lieyang Chen, Anthony Cruz, Steven Ramsey, +5

Artificial IntelligenceConvolutional Neural NetworkEngineeringMachine LearningAutoencoders +19

High-resolution structures of multiple 5-HT3AR-setron complexes reveal a novel mechanism of competitive inhibition

Sandip Basak, Arvind Kumar, Steven Ramsey, +4

eLife

Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces

Kamran Haider, Lauren Wickstrom, Steven Ramsey, +2

The Journal of Physical Chemistry B

Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water

Sang Won Jung, Minsup Kim, Steven Ramsey, +2

Scientific Reports

Mechanism of μ-Opioid Receptor-Magnesium Interaction and Positive Allosteric Modulation

Xiaohu Hu, Davide Provasi, Steven Ramsey, +1

Biophysical Journal

Molecular PharmacologyPositive Allosteric ModulationMedicinePhysiologyMechanism Of Action +3

Predicted Mode of Binding to and Allosteric Modulation of the μ-Opioid Receptor by Kratom’s Alkaloids with Reported Antinociception <i>In Vivo</i>

Yuchen Zhou, Steven Ramsey, Davide Provasi, +7

Biochemistry