A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models. - Mette Alstrup Lie; Birgit Schiøtt (J. Comput. Chem., 2008)

Molecular Docking with Ligand Attached Water Molecules. - Mette Alstrup Lie; René Thomsen; Christian N. S. Pedersen; Birgit Schiøtt; Mikael H. Christensen (J. Chem. Inf. Model., 2011)

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na+ Ion Release. - Heidi Koldsø; Pernille Noer; Julie Grouleff; Henriette Elisabeth Autzen; Steffen Sinning; Birgit Schiøtt (PLoS Comput. Biol., 2011)

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition. - Talia Zeppelin; Lucy Kate Ladefoged; Steffen Sinning; Xavier Periole; Birgit Schiøtt (PLoS Comput. Biol., 2018)

Molecular Modeling Investigation of the Interaction between Humicola insolens Cutinase and SDS Surfactant Suggests a Mechanism for Enzyme Inactivation. - Lisbeth Ravnkilde Kjølbye; Anne Laustsen; Mikkel Vestergaard; Xavier Periole; Leonardo De Maria; Allan Svendsen; Andrea Coletta; Birgit Schiøtt (J. Chem. Inf. Model., 2019)

General Protocol for Constructing Molecular Models of Nanodiscs. - Lisbeth Ravnkilde Kjølbye; Leonardo De Maria; Tsjerk A. Wassenaar; Haleh Abdizadeh; Siewert J. Marrink; Jesper Ferkinghoff-Borg; Birgit Schiøtt (J. Chem. Inf. Model., 2021)

Beneficent and Maleficent Effects of Cations on Bufadienolide Binding to Na+, K+-ATPase. - Lucy Kate Ladefoged; Birgit Schiøtt; Natalya U. Fedosova (J. Chem. Inf. Model., 2021)

Lipid Modulation of a Class B GPCR: Elucidating the Modulatory Role of PI(4, 5)P2 Lipids. - Lisbeth Ravnkilde Kjølbye; Lars Sørensen; Jun Yan; Nils A. Berglund; Jesper Ferkinghoff-Borg; Carol V. Robinson; Birgit Schiøtt (J. Chem. Inf. Model., 2022)

Creating Coarse-Grained Systems with COBY: Toward Higher Accuracy of Complex Biological Systems. - Mikkel D. Andreasen; Paulo C. T. Souza; Birgit Schiøtt; Lorena Zuzic (J. Chem. Inf. Model., 2025)

Permeability Benchmarking: Guidelines for Comparing in Silico, in Vitro, and in Vivo Measurements. - Christian Jorgensen; Raleigh M. Linville; Ian Galea; Edward Lambden; Martin Vögele; Charles Chen; Evan P. Troendle; Fiorella Ruggiu; Martin B. Ulmschneider; Birgit Schiøtt; Christian D. Lorenz (J. Chem. Inf. Model., 2025)