A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). - Giovanni Bottegoni; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2008)

Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods. - Hui Sun Lee; Jiwon Choi; Irina Kufareva; Ruben Abagyan; Anton V. Filikov; Young Yang; Sukjoon Yoon (J. Chem. Inf. Model., 2008)

Spatial chemical distance based on atomic property fields. - A. V. Grigoryan; Irina Kufareva; Maxim Totrov; Ruben Abagyan (J. Comput. Aided Mol. Des., 2010)

Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. - So-Jung Park; Irina Kufareva; Ruben Abagyan (J. Comput. Aided Mol. Des., 2010)

Pocketome: an encyclopedia of small-molecule binding sites in 4D. - Irina Kufareva; Andrey V. Ilatovskiy; Ruben Abagyan (Nucleic Acids Res., 2012)

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)

Structure-Based Predictions of Activity Cliffs. - Jarmila Husby; Giovanni Bottegoni; Irina Kufareva; Ruben Abagyan; Andrea Cavalli (J. Chem. Inf. Model., 2015)

Druggable exosites of the human kino-pocketome. - George Nicola; Irina Kufareva; Andrey V. Ilatovskiy; Ruben Abagyan (J. Comput. Aided Mol. Des., 2020)

kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models. - Willow Carretero Chavez; Marcus Krantz; Edda Klipp; Irina Kufareva (BMC Bioinform., 2023)