Catalytic Site p<i>K</i>_a Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations

Florian Hofer, Johannes Kraml, Ursula Kahler, +2

Journal of Chemical Information and Modeling

Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties

Monica L. Fernández‐Quintero, Johannes R. Loeffler, Johannes Kraml, +3

Frontiers in Immunology

Protein AssemblyProtein FoldingConformational EnsemblesNatural SciencesMolecular Biology +13

Polarizable and non-polarizable force fields: Protein folding, unfolding, and misfolding

Anna S. Kamenik, Philip H. Handle, Florian Hofer, +3

The Journal of Chemical Physics

Protein AssemblyMolecular BiologyProtein RefoldingMolecular DynamicsSingle Molecule Biophysics +17

Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin

Ursula Kahler, Anna S. Kamenik, Franz Waibl, +2

Biophysical Journal

Protein AssemblyMolecular BiologyEncounter PosesMolecular DynamicsDrug Discovery Efforts +19

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

Julian E. Fuchs, Roland G. Huber, Birgit J. Waldner, +4

PLoS ONE

Protein AssemblyMolecular BiologyMolecular DynamicsConformational SelectionProtein Folding +16

Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference

Vedat Durmaz, Katharina Köchl, A. Krassnigg, +15

Scientific Reports

Macrocycle Cell Permeability Measured by Solvation Free Energies in Polar and Apolar Environments

Anna S. Kamenik, Johannes Kraml, Florian Hofer, +5

Journal of Chemical Information and Modeling

EngineeringPolar EnvironmentsComputational ChemistryCell BiophysicsMolecular Dynamics +14

Localization of Millisecond Dynamics: Dihedral Entropy from Accelerated MD

Anna S. Kamenik, Ursula Kahler, Julian E. Fuchs, +1

Journal of Chemical Theory and Computation

EngineeringBiomolecular Structure PredictionMolecular BiologyLocal DynamicsMolecular Dynamics +18

Solvation Thermodynamics in Different Solvents: Water–Chloroform Partition Coefficients from Grid Inhomogeneous Solvation Theory

Johannes Kraml, Florian Hofer, Anna S. Kamenik, +4

Journal of Chemical Information and Modeling

Reliable InformationEngineeringChemical AnalysisComputational ChemistryChemistry +20

Electrostatic recognition in substrate binding to serine proteases

Birgit J. Waldner, Johannes Kraml, Ursula Kahler, +6

Journal of Molecular Recognition