Personal Websites

Petr Popov

Dr. Petr Popov received PhD in Applied Math and Computer Science at Inria – Grenoble Rhone-Alpes, where he was developing algorithms for molecular modelling and computational chemistry in the Nano-D team. Later Dr. Popov joined Moscow Institute of Physics and Technology and the Bridge Institute of University of Southern California, where he developed structure analysis and machine learning tools to study structure and function of transmembrane proteins. Dr. Popov contributed to the structure determination of G protein-coupled receptors, which are one of the most important pharmacological targets, resulting in publications in top-ier scientific journals. His research mainly focuses on digital platforms for intelligent pharma applications.

For more information about current research please visit iMolecule and check our selected publications .
There are also open positions in our group for PhD and MSc students.
  • Machine learning applied for molecular structures
  • Computational biomolecular modelling and design
  • Computer-aided drug discovery

Journal articles

  1. Popov, Petr, et al. “Controlled‐advancement rigid‐body optimization of nanosystems.” Journal of computational chemistry 40.27 (2019): 2391-2399.
  2. Luginina, Aleksandra, et al. “Structure-based mechanism of cysteinyl leukotriene receptor inhibition by antiasthmatic drugs.” Science Advances 5.10 (2019): eaax2518.
  3. Popov, Petr, et al. “Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure.” PloS one 14.7 (2019).
  4. Popov, Petr, et al. “Computational design for thermostabilization of GPCRs.” Current Opinion in Structural Biology 55 (2019): 25-33
  5. Li, Xiaoting, et al. “Crystal Structure of the Human Cannabinoid Receptor CB2.” Cell 176.3 (2019): 459-467.
  6. Audet, Martin, et al. “Crystal structure of misoprostol bound to the labor inducer prostaglandin E 2 receptor.” Nature chemical biology (2019): 1.
  7. Yang, Shifan, et al. “Crystal structure of the Frizzled 4 receptor in a ligand-free state.” Nature 560.7720 (2018): 666.
  8. Popov, Petr, et al. “Computational design of thermostabilizing point mutations for G protein-coupled receptors.” eLife 7 (2018): e34729.
  9. Peng, Yao, et al. “5-HT2C receptor structures reveal the structural basis of GPCR polypharmacology.” Cell 172.4 (2018): 719-730.
  10. Popov, Petr et al. “Eurecon: Equidistant uniform rigid-body ensemble constructor.” Journal of Molecular Graphics and Modelling 80 (2018): 313-319.
  11. Neveu, Emilie, et al. “RapidRMSD: Rapid determination of RMSDs corresponding to motions of flexible molecules.” Bioinformatics (2018).
  12. Batyuk, Alexander, et al. “Native phasing of x-ray free-electron laser data for a G protein–coupled receptor.” Science Advances 2.9 (2016): e1600292.
  13. Neveu, Emilie, et al. “PEPSI-Dock: a detailed data-driven protein–protein interaction potential accelerated by polar Fourier correlation.” Bioinformatics 32.17 (2016): i693-i701.
  14. Lensink, Marc F., et al. “Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: A CASP‐CAPRI experiment.” Proteins: Structure, Function, and Bioinformatics (2016).
  15. S Grudinin et al., Predicting binding poses and affinities in the CSAR 2013-2014 docking exercises using the knowledge-based Convex-PL potential, Journal of Chemical Information and Modeling, 2015.
  16. P Popov et al., Knowledge of Native Protein–Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates, Journal of Chemical Information and Modeling, 2015.
  17. P Popov et al., Rapid determination of RMSDs corresponding to macromolecular rigid body motions, Journal of computational chemistry, 2014.
  18. P Popov et al., DockTrina: Docking triangular protein trimers, Proteins: Structure, Function, and Bioinformatics, 2014.
  19. Moretti, Rocco, et al. “Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions.” Proteins: Structure, Function, and Bioinformatics 81.11 (2013): 1980-1987.
  • Alexander Morozov (PhD student, Skoltech)
  • Igor Kozlovskii (MSc student, MIPT)
  • Mark Zaretskii (MSc student, MIPT)
  • Alena Buglakova (MSc student, Skoltech)
  • Semen Glushkov (MSc student, Skoltech/MIPT)
Georgy Derevyanko
Junior Research Scientist

“Machine learning in Chemoinformatics”, Term 4/8, 3 ECTS.