Virtual screening using structure-based consensus pharmacophore models and ensemble docking based on MD-generated conformations. - Oliver Koch; Daniel Cappel; Monika Nocker; Timo Jäger; Leopold Flohé; Christoph A. Sotriffer; Paul M. Selzer (J. Cheminformatics, 2011)

Generation of structure-based pharmacophores using energetic analysis - application on fragment docking. - Kathryn Loving; Noeris K. Salam; Daniel Cappel; Woody Sherman (J. Cheminformatics, 2011)

Probing the Dynamic Nature of Water Molecules and Their Influences on Ligand Binding in a Model Binding Site. - Daniel Cappel; Rickard Wahlström; Ruth Brenk; Christoph A. Sotriffer (J. Chem. Inf. Model., 2011)

Impact of binding site waters on inhibitor design: contemplating a novel inverse binding mode of indirubin derivatives in DYRK kinases. - Daniel Cappel; Vassilios Myrianthopoulos; Emmanuel Mikros; Woody Sherman (J. Cheminformatics, 2014)

Exploring conformational search protocols for ligand-based virtual screening and 3-D QSAR modeling. - Daniel Cappel; Steven L. Dixon; Woody Sherman; Jianxin Duan (J. Comput. Aided Mol. Des., 2015)

Accurate Binding Free Energy Predictions in Fragment Optimization. - Thomas B. Steinbrecher; Markus K. Dahlgren; Daniel Cappel; Teng Lin; Lingle Wang; Goran Krilov; Robert Abel; Richard A. Friesner; Woody Sherman (J. Chem. Inf. Model., 2015)

Relative Binding Free Energy Calculations Applied to Protein Homology Models. - Daniel Cappel; Michelle Lynn Hall; Eelke B. Lenselink; Thijs Beuming; Jun Qi; James Bradner; Woody Sherman (J. Chem. Inf. Model., 2016)

Impact of Different Automated Binding Pose Generation Approaches on Relative Binding Free Energy Simulations. - Daniel Cappel; Steven Jerome; Gerhard Hessler; Hans Matter (J. Chem. Inf. Model., 2020)

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects. - Christina E. M. Schindler; Hannah M. Baumann; Andreas Blum; Dietrich Böse; Hans-Peter Buchstaller; Lars Burgdorf; Daniel Cappel; Eugene Chekler; Paul Czodrowski; Dieter Dorsch; Merveille K. I. Eguida; Bruce Follows; et al. (J. Chem. Inf. Model., 2020)

Performance of Relative Binding Free Energy Calculations on an Automatically Generated Dataset of Halogen-Deshalogen Matched Molecular Pairs. - Daniel Cappel; Jean-Christophe Mozziconacci; Tatjana Braun; Thomas Steinbrecher (J. Chem. Inf. Model., 2021)