The importance of template choice in homology modeling. A 5-HT6R case study. - Krzysztof Rataj; Jagna Witek; Stefan Mordalski; Tomasz Kosciólek; Andrzej J. Bojarski (J. Cheminformatics, 2013)

Application of Structural Interaction Fingerpints (SIFts) into post-docking analysis - insight into activity and selectivity. - Jagna Witek; Krzysztof Rataj; Stefan Mordalski; Sabina Smusz; Tomasz Kosciólek; Andrzej J. Bojarski (J. Cheminformatics, 2013)

Impact of Template Choice on Homology Model Efficiency in Virtual Screening. - Krzysztof Rataj; Jagna Witek; Stefan Mordalski; Tomasz Kosciólek; Andrzej J. Bojarski (J. Chem. Inf. Model., 2014)

Compounds Activity Prediction in Large Imbalanced Datasets with Substructural Relations Fingerprint and EEM. - Wojciech Marian Czarnecki; Krzysztof Rataj (TrustCom/BigDataSE/ISPA (2), 2015)

Multiple conformational states in retrospective virtual screening - homology models vs. crystal structures: beta-2 adrenergic receptor case study. - Stefan Mordalski; Jagna Witek; Sabina Smusz; Krzysztof Rataj; Andrzej J. Bojarski (J. Cheminformatics, 2015)

Multi-Step Protocol for Automatic Evaluation of Docking Results Based on Machine Learning Methods - A Case Study of Serotonin Receptors 5-HT6 and 5-HT7. - Sabina Smusz; Stefan Mordalski; Jagna Witek; Krzysztof Rataj; Rafal Kafel; Andrzej J. Bojarski (J. Chem. Inf. Model., 2015)

GPCRdb: an information system for G protein-coupled receptors. - Vignir Ísberg; Stefan Mordalski; Christian Munk; Krzysztof Rataj; Kasper Harpsøe; Alexander S. Hauser; Bas Vroling; Andrzej J. Bojarski; Gert Vriend; David E. Gloriam (Nucleic Acids Res., 2016)

From Homology Models to a Set of Predictive Binding Pockets-a 5-HT1A Receptor Case Study. - Dawid Warszycki; Manuel Rueda; Stefan Mordalski; Kurt Kristiansen; Grzegorz Satala; Krzysztof Rataj; Zdzislaw Chilmonczyk; Ingebrigt Sylte; Ruben Abagyan; Andrzej J. Bojarski (J. Chem. Inf. Model., 2017)

Salt Bridge in Ligand-Protein Complexes - Systematic Theoretical and Statistical Investigations. - Rafal Kurczab; Pawel Sliwa; Krzysztof Rataj; Rafal Kafel; Andrzej J. Bojarski (J. Chem. Inf. Model., 2018)

Mol-CycleGAN - A Generative Model for Molecular Optimization. - Lukasz Maziarka; Agnieszka Pocha; Jan Kaczmarczyk; Krzysztof Rataj; Michal Warchol (ICANN (Workshop), 2019)

Molecule Attention Transformer. - Lukasz Maziarka; Tomasz Danel; Slawomir Mucha; Krzysztof Rataj; Jacek Tabor; Stanislaw Jastrzebski (CoRR, 2020)

Mol-CycleGAN: a generative model for molecular optimization. - Lukasz Maziarka; Agnieszka Pocha; Jan Kaczmarczyk; Krzysztof Rataj; Tomasz Danel; Michal Warchol (J. Cheminformatics, 2020)