Molecular Query Language (MQL)A Context-Free Grammar for Substructure Matching. - Ewgenij Proschak; Jörg K. Wegner; Andreas Schüller; Gisbert Schneider; Uli Fechner (J. Chem. Inf. Model., 2007)

Kernel Approach to Molecular Similarity Based on Iterative Graph Similarity. - Matthias Rupp; Ewgenij Proschak; Gisbert Schneider (J. Chem. Inf. Model., 2007)

Shapelets: Possibilities and limitations of shape-based virtual screening. - Ewgenij Proschak; Matthias Rupp; Swetlana Derksen; Gisbert Schneider (J. Comput. Chem., 2008)

PhAST: Pharmacophore alignment search tool. - Volker Hähnke; Bettina Hofmann; Tomislav Grgat; Ewgenij Proschak; Dieter Steinhilber; Gisbert Schneider (J. Comput. Chem., 2009)

Reaction-MQL: Line Notation for Functional Transformation. - Felix Reisen; Gisbert Schneider; Ewgenij Proschak (J. Chem. Inf. Model., 2009)

Protein-protein docking by shape-complementarity and property matching. - Tim Geppert; Ewgenij Proschak; Gisbert Schneider (J. Comput. Chem., 2010)

SBE13, a newly identified inhibitor of inactive polo-like kinase 1. - Sarah Keppner; Ewgenij Proschak; Gisbert Schneider; Birgit Spänkuch (J. Cheminformatics, 2010)

Kernel learning for ligand-based virtual screening: discovery of a new PPARγ agonist. - Matthias Rupp; Timon Schroeter; Ramona Steri; Ewgenij Proschak; Katja Hansen; Heiko Zettl; Oliver Rau; Manfred Schubert-Zsilavecz; Klaus-Robert Müller; Gisbert Schneider (J. Cheminformatics, 2010)

Rational, computer-aided design of multi-target ligands. - Janosch Achenbach; Ewgenij Proschak (J. Cheminformatics, 2011)

Fragment-based identification of multi-target ligands by self-organizing map alignment. - Janosch Achenbach; Franca-Maria Klingler; Steffen Hahn; Svenja Steinbrink; Mirjam Schroeder; Frank Loehr; Volker Dötsch; Dieter Steinhilber; Ewgenij Proschak (J. Cheminformatics, 2012)

Design of dual ligands using excessive pharmacophore query alignment. - Daniel Moser; Joanna Wisniewska; Steffen Hahn; Estel la Buscató; Franca-Maria Klingler; Janosch Achenbach; Bettina Hofmann; Dieter Steinhilber; Ewgenij Proschak (J. Cheminformatics, 2012)

DOGS: Reaction-Driven de novo Design of Bioactive Compounds. - Markus Hartenfeller; Heiko Zettl; Miriam Walter; Matthias Rupp; Felix Reisen; Ewgenij Proschak; Sascha Weggen; Holger Stark; Gisbert Schneider (PLoS Comput. Biol., 2012)

In silico polypharmacology: retrospective recognition vs. rational design. - Ewgenij Proschak (J. Cheminformatics, 2014)

PENG: A Neural Gas-Based Approach for Pharmacophore Elucidation. Method Design, Validation, and Virtual Screening for Novel Ligands of LTA4H. - Daniel Moser; Sandra K. Wittmann; Jan Kramer; René Blöcher; Janosch Achenbach; Denys Pogoryelov; Ewgenij Proschak (J. Chem. Inf. Model., 2015)

VAMMPIRE-LORD: A Web Server for Straightforward Lead Optimization Using Matched Molecular Pairs. - Julia Weber; Janosch Achenbach; Daniel Moser; Ewgenij Proschak (J. Chem. Inf. Model., 2015)