Rapid binding site analysis by means of structural interaction fingerprint patterns - an implication to GPCR-targeted CADD. - Tomasz Kosciólek; Stefan Mordalski; Andrzej J. Bojarski (J. Cheminformatics, 2011)

Evaluation of different machine learning methods for ligand-based virtual screening. - Rafal Kurczab; Sabina Smusz; Andrzej J. Bojarski (J. Cheminformatics, 2011)

Homology modelling of metabotropic glutamate receptor 2. - Stefan Mordalski; Tomasz Kosciólek; Aina Westrheim Ravna; Ingebrigt Sylte; Andrzej J. Bojarski (J. Cheminformatics, 2011)

The influence of training actives/inactives ratio on machine learning performance. - Rafal Kurczab; Sabina Smusz; Andrzej J. Bojarski (J. Cheminformatics, 2013)

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)

The influence of the inactives subset generation on the performance of machine learning methods. - Sabina Smusz; Rafal Kurczab; Andrzej J. Bojarski (J. Cheminformatics, 2013)

The influence of hashed fingerprints density on the machine learning methods performance. - Sabina Smusz; Rafal Kurczab; 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)

New Strategy for Receptor-Based Pharmacophore Query Construction: A Case Study for 5-HT7 Receptor Ligands. - Rafal Kurczab; Andrzej J. Bojarski (J. Chem. Inf. Model., 2013)

The influence of negative training set size on machine learning-based virtual screening. - Rafal Kurczab; Sabina Smusz; Andrzej J. Bojarski (J. Cheminformatics, 2014)

Identification of Novel Serotonin Transporter Compounds by Virtual Screening. - Mari Gabrielsen; Rafal Kurczab; Agata Siwek; Malgorzata Wolak; Aina Westrheim Ravna; Kurt Kristiansen; Irina Kufareva; Ruben Abagyan; Gabriel Nowak; Zdzislaw Chilmonczyk; Ingebrigt Sylte; Andrzej J. Bojarski (J. Chem. Inf. Model., 2014)

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)

Robust optimization of SVM hyperparameters in the classification of bioactive compounds. - Wojciech M. Czarnecki; Sabina Podlewska; Andrzej J. Bojarski (J. Cheminformatics, 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)

Ligand-Based Virtual Screening in a Search for Novel Anti-HIV-1 Chemotypes. - Agata Kurczyk; Dawid Warszycki; Robert Musiol; Rafal Kafel; Andrzej J. Bojarski; Jaroslaw Polanski (J. Chem. Inf. Model., 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)

Creating the New from the Old: Combinatorial Libraries Generation with Machine-Learning-Based Compound Structure Optimization. - Sabina Podlewska; Wojciech M. Czarnecki; Rafal Kafel; Andrzej J. Bojarski (J. Chem. Inf. Model., 2017)

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)

GPCRdb in 2018: adding GPCR structure models and ligands. - Gáspár Pándy-Szekeres; Christian Munk; Tsonko M. Tsonkov; Stefan Mordalski; Kasper Harpsøe; Alexander S. Hauser; Andrzej J. Bojarski; David E. Gloriam (Nucleic Acids Res., 2018)

Development of New Methods Needs Proper Evaluation - Benchmarking Sets for Machine Learning Experiments for Class A GPCRs. - Damian Lesniak; Sabina Podlewska; Stanislaw Jastrzebski; Igor Sieradzki; Andrzej J. Bojarski; Jacek Tabor (J. Chem. Inf. Model., 2019)

Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening. - Stanislaw Jastrzebski; Maciej Szymczak; Agnieszka Pocha; Stefan Mordalski; Jacek Tabor; Andrzej J. Bojarski; Sabina Podlewska (J. Chem. Inf. Model., 2020)

2D SIFt: a matrix of ligand-receptor interactions. - Stefan Mordalski; Agnieszka Wojtuch; Igor T. Podolak; Rafal Kurczab; Andrzej J. Bojarski (J. Cheminformatics, 2021)