A simple way to calculate the axis of an -helix. - Johan Åqvist (Comput. Chem., 1986)

Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. - Johan Åqvist (J. Comput. Chem., 1996)

Ligand binding affinity prediction by linear interaction energy methods. - Tomas Hansson; John Marelius; Johan Åqvist (J. Comput. Aided Mol. Des., 1998)

Computation of affinity and selectivity: Binding of 2, 4-diaminopteridine and 2, 4-diaminoquinazoline inhibitors to dihydrofolate reductases. - John Marelius; Malin Graffner-Nordberg; Tomas Hansson; Anders Hallberg; Johan Åqvist (J. Comput. Aided Mol. Des., 1998)

Binding affinity prediction with different force fields: Examination of the linear interaction energy method. - Martin Almlöf; Bjørn Olav Brandsdal; Johan Åqvist (J. Comput. Chem., 2004)

Computational Prediction of Structure-Activity Relationships for the Binding of Aminocyclitols to β-Glucocerebrosidase. - Lucía Díaz; Jordi Bujons; Antonio Delgado; Hugo Gutiérrez-de-Terán; Johan Åqvist (J. Chem. Inf. Model., 2011)

Computational prediction of monosaccharide binding free energies to lectins with linear interaction energy models. - Sushil Kumar Mishra; Johan Sund; Johan Åqvist; Jaroslav Koca (J. Comput. Chem., 2012)

Toward an Optimal Docking and Free Energy Calculation Scheme in Ligand Design with Application to COX-1 Inhibitors. - Yasmin Shamsudin Khan; Hugo Gutiérrez-de-Terán; Lars Boukharta; Johan Åqvist (J. Chem. Inf. Model., 2014)

Computational Prediction of Alanine Scanning and Ligand Binding Energetics in G-Protein Coupled Receptors. - Lars Boukharta; Hugo Gutiérrez-de-Terán; Johan Åqvist (PLoS Comput. Biol., 2014)

Protein Surface Softness Is the Origin of Enzyme Cold-Adaptation of Trypsin. - Geir Villy Isaksen; Johan Åqvist; Bjørn Olav Brandsdal (PLoS Comput. Biol., 2014)

Q6: A comprehensive toolkit for empirical valence bond and related free energy calculations. - Paul Bauer; Alexandre Barrozo; Miha Purg; Beat Anton Amrein; Mauricio Esguerra; Philippe Barrie Wilson; Dan Thomas Major; Johan Åqvist; Shina Caroline Lynn Kamerlin (SoftwareX, 2018)

QligFEP: an automated workflow for small molecule free energy calculations in Q. - Willem Jespers; Mauricio Esguerra; Johan Åqvist; Hugo Gutiérrez-de-Terán (J. Cheminformatics, 2019)

Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. - Willem Jespers; Laura H. Heitman; Adriaan P. IJzerman; Eddy Sotelo; Gerard J. P. van Westen; Johan Åqvist; Hugo Gutiérrez-de-Terán (PLoS Comput. Biol., 2021)