Publications

2025

• NanoDeNovo: de novo design of anti-poliovirus I Sabin strain nanobodies by semi-automated computational pipeline Kotelnikov D. D., Tatarinova K. S., Zhdanov D. D. International Journal of Molecular Sciences, 26(19), art. 9262 · 10.3390/ijms26199262
• Gold(III) complexes containing (non)protonated oligopyridines — unexpected results in cancer drug research Koshenskova K. A., Bardina E. E., Makotchenko E. V., …, Kotel'nikov D. D., …, Lutsenko I. A. New Journal of Chemistry, 49(32), 14037–14052 · 10.1039/D5NJ02110C
• The eusocial non-code: unveiling the impact of noncoding RNAs on Hymenoptera eusocial evolution Lebedev E., Smutin D., Timkin P., Kotelnikov D., Taldaev A., Panushev N., Adonin L. Non-Coding RNA Research, 11, 48–59 · 10.1016/j.ncrna.2024.10.007
• Molecular interactions between ZnO nanoparticles and liver target proteins revealed by molecular docking method Kirichenko K. Yu., Pamirsky I. E., Timkin P. D., Kotelnikov D. D. et al. BioNanoScience, 15, art. 94 · 10.1007/s12668-024-01665-w
• Intermolecular interactions of graphene nanosheets with enzymes of the Danio rerio antioxidant system Timkin P. D., Kotelnikov D. D. et al. Nanobiotechnology Reports, 20(suppl. 1), S199–S203 · 10.1134/S2635167625602396
• Structural features of binding of single-wall carbon nanotubes with enzymes of the antioxidant system of Danio rerio Timkin P. D. et al. Nanobiotechnology Reports, 20(suppl. 1), S114–S118 · 10.1134/S2635167625602360
• Study of intermolecular interactions of an enzyme of the antioxidant system of Danio rerio with CdS and ZnS nanoparticles Timkin P. D. et al. Nanobiotechnology Reports, 20(suppl. 1), S119–S123 · 10.1134/S2635167625602372
• Differential analysis of glycinin and β-conglycinin gene expression in seeds of cultivated soybean varieties at different periods of their maturation Penzin A. A., Timkin P. D., Kotelnikov D. D. Siberian Journal of Life Sciences and Agriculture, 17(3), 56–70 · 10.12731/2658-6649-2025-17-3-1208
• In silico study of the molecular mechanisms of iron oxide nanoparticle toxicity towards Heterosigma akashiwo and Porphyridium purpureum Kirichenko K. Yu., Pamirsky I. E., Timofeev E. A., Kotelnikov D. D. et al. Industrial Processes and Technologies, 5(4/18), 38–53 · 10.37816/2713-0789-2025-5-4(18)-38-53

2024

• Study of molecular interactions of synthetic glucocorticoids with TRPM8 by molecular docking Timkin P. D., Kotelnikov D. D., Timofeev E. A., Naumov D. E., Borodin E. A. Bulletin of Siberian Medicine, 23(4), 136–144 · 10.20538/1682-0363-2024-4-136-144
• Development and evaluation of primers for the analysis of glycinin subunit transcripts of Glycine max (L.) Merr. Timkin P. D., Kotelnikov D. D., Penzin A. A., Statsenko S. S. Fodder Production, 9, 12–18 · 10.30906/1562-0417-2024-9-12-18
• RNA interference in silico: siRNA design and molecular dynamics of a protein–RNA complex in prion disease Linskaya P. M., Kotelnikov D. D., Demenchuk Ya. V. 3rd Annual School of Young Researchers in Genetic Technologies, 20–23 · EDN VKZQCR

2023

• In silico prediction of transcription factor–enhancer interaction as the first stage of axonal growth regulation Kotelnikov D. D., Sinyokin I. A., Borodin E. A., Batalova T. A. Sechenov Medical Journal, 14(4), 42–50 · 10.47093/2218-7332.2023.907.12
• Copper(II) furancarboxylate complexes with 5-nitro-1,10-phenanthroline as promising biological agents Koshenskova K. A., Baravikov D. E., Nelyubina Yu. V., …, Kotel'nikov D. D., …, Lutsenko I. A. Russian Journal of Coordination Chemistry, 49(10), 660–671 · 10.1134/S1070328423600730
• Study of the molecular mechanisms of herbicide binding to target proteins of weeds by in silico methods Pamirsky I. E., Timkin P. D., Timofeev E. A., Kotelnikov D. D. et al. Russian Agricultural Sciences, 49(4), 374–384 · 10.3103/S1068367423040110