Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge. - Mikhail Ignatov; Cong Liu 031; Andrey Alekseenko; Zhuyezi Sun; Dzmitry Padhorny; Sergei Kotelnikov; Andrey M. Kazennov; Ivan Grebenkin; Yaroslav Kholodov; Istvan Kolosvari; Alberto Pérez; Ken A. Dill; et al. (J. Comput. Aided Mol. Des., 2019)

Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4. - Sergei Kotelnikov; Andrey Alekseenko; Cong Liu 031; Mikhail Ignatov; Dzmitry Padhorny; Emiliano Brini; Mark Lukin; Evangelos A. Coutsias; Ken A. Dill; Dima Kozakov (J. Comput. Aided Mol. Des., 2020)

Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles. - Xin Cao; Mikhail Ignatov; George Jones; Sara N. Pollock; Evangelos A. Coutsias; Dima Kozakov (BCB, 2023)

Improved prediction of MHC-peptide binding using protein language models. - Nasser Hashemi; Boran Hao; Mikhail Ignatov; Ioannis Ch. Paschalidis; Pirooz Vakili; Sandor Vajda; Dima Kozakov (Frontiers Bioinform., 2023)