Comparison of multiple Amber force fields and development of improved protein backbone parameters

Viktor Horn̆ák, Robert Abel, Asim Okur, +3

Proteins Structure Function and Bioinformatics

HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

Viktor Horn̆ák, Asim Okur, Robert C. Rizzo, +1

Proceedings of the National Academy of Sciences

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

Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex

Dirksen E. Bussiere, Lili Xie, Honnappa Srinivas, +24

Nature Chemical Biology

Signal TransductionMolecular ResearchMolecular RegulationMedicineNatural Sciences +8

Crystallographic Structure of the K Intermediate of Bacteriorhodopsin: Conservation of Free Energy after Photoisomerization of the Retinal

Brigitte Schobert, Jill R. Cupp‐Vickery, Viktor Horn̆ák, +2

Journal of Molecular Biology

Free EnergyPhotoreceptor CellK IntermediateBiochemistryPhotochemistry +9

Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation

Shivani Ahuja, Viktor Horn̆ák, Elsa C. Y. Yan, +9

Nature Structural & Molecular Biology

Biophysical ModelingProtein FunctionSignal TransductionMolecular PhysiologyBiochemistry +12

Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model

Asim Okur, Lauren Wickstrom, Melinda Layten, +4

Journal of Chemical Theory and Computation

Chemical KineticsEngineeringComputational ChemistryChemistryMolecular Dynamics +14

Secondary Structure Bias in Generalized Born Solvent Models:  Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation

Daniel R. Roe, Asim Okur, Lauren Wickstrom, +2

The Journal of Physical Chemistry B

Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

Callum J. Dickson, Viktor Horn̆ák, Robert A. Pearlstein, +1

Journal of the American Chemical Society

Membrane StructureComputational BiophysicsMolecular DynamicsMembrane Flip-flop RateBiochemistry +10

Location of Trp265 in Metarhodopsin II: Implications for the Activation Mechanism of the Visual Receptor Rhodopsin

Evan Crocker, Markus Eilers, Shivani Ahuja, +4

Journal of Molecular Biology

Metarhodopsin IiMolecular PhysiologySignal TransductionBiochemistryG Protein-coupled Receptor +10