Docking small ligands in flexible binding sites. - Joannis Apostolakis; Andreas Plückthun; Amedeo Caflisch (J. Comput. Chem., 1998)

A simple approach for protein name identification: prospects and limits. - Katrin Fundel; Daniel Güttler; Ralf Zimmer; Joannis Apostolakis (BMC Bioinform., 2005)

Fully Automated Flexible Docking of Ligands into Flexible Synthetic Receptors Using Forward and Inverse Docking Strategies. - Andreas Kämper; Joannis Apostolakis; Matthias Rarey; Christel M. Marian; Thomas Lengauer (J. Chem. Inf. Model., 2006)

Graph-Based Molecular Alignment (GMA). - Jörn Marialke; Robert Körner; Simon Tietze; Joannis Apostolakis (J. Chem. Inf. Model., 2007)

GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes. - Simon Tietze; Joannis Apostolakis (J. Chem. Inf. Model., 2007)

Automatic Determination of Reaction Mappings and Reaction Center Information. 2. Validation on a Biochemical Reaction Database. - Joannis Apostolakis; Oliver Sacher; Robert Körner; Johann Gasteiger (J. Chem. Inf. Model., 2008)

Automatic Determination of Reaction Mappings and Reaction Center Information. 1. The Imaginary Transition State Energy Approach. - Robert Körner; Joannis Apostolakis (J. Chem. Inf. Model., 2008)

Similarity Based Docking. - Jörn Marialke; Simon Tietze; Joannis Apostolakis (J. Chem. Inf. Model., 2008)

De Novo Drug Design Using Multiobjective Evolutionary Graphs. - Christos A. Nicolaou; Joannis Apostolakis; Constantinos S. Pattichis (J. Chem. Inf. Model., 2009)