Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

Devleena Shivakumar, Joshua Williams, Yujie Wu, +3

Journal of Chemical Theory and Computation

Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field

Lingle Wang, Yujie Wu, Yuqing Deng, +26

Journal of the American Chemical Society

Drug TargetEngineeringComputational ChemistryMolecular DynamicsMolecular Design +24

Flexible simple point-charge water model with improved liquid-state properties

Yujie Wu, Harald L. Tepper, Gregory A. Voth

The Journal of Chemical Physics

ElectrohydrodynamicsEngineeringLiquid-liquid FlowComputational ChemistryChemistry +15

An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport

Yujie Wu, Hanning Chen, Feng Wang, +2

The Journal of Physical Chemistry B

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors

Lingle Wang, Yuqing Deng, Jennifer L. Knight, +6

Journal of Chemical Theory and Computation

Drug TargetFep/rest ResultsEngineeringLocal Structural RearrangementsMolecular Biology +19

Lead optimization mapper: automating free energy calculations for lead optimization

Shuai Liu, Yujie Wu, Lin Teng, +6

Journal of Computer-Aided Molecular Design

Mathematical ProgrammingModel OptimizationComputational ScienceLarge-scale Global OptimizationEngineering +6

Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery

Lingle Wang, Yuqing Deng, Yujie Wu, +6

Journal of Chemical Theory and Computation

Scaffold HoppingEngineeringProtein FoldingDrug DiscoveryMedicine +11

Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges

Wei Chen, Yuqing Deng, Ellery Russell, +3

Journal of Chemical Theory and Computation

Proton Transport Behavior through the Influenza A M2 Channel: Insights from Molecular Simulation

Hanning Chen, Yujie Wu, Gregory A. Voth

Biophysical Journal

Biophysical ModelingProton TransferProton Transport BehaviorMolecular BiologyVirology +3

Charge Delocalization in Proton Channels, I: The Aquaporin Channels and Proton Blockage

Hanning Chen, Boaz Ilan, Yujie Wu, +3

Biophysical Journal

OsmoregulationProton ChannelsBiochemistryProton-coupled Electron TransferProton Transfer +8