dmitryshcherbinin

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Dmitry Shcherbinin

Professor: Dmitri Papatsenko

Dmitrii graduated from Moscow State University, School of Bioengineering and Bioinformatics in 2007.

After that he made his Ph.D. work in Mathematical Biology and Bioinformatics in the  Institute of Biomedical Chemistry and defended doctoral thesis in 2013.

In his research he specialized in structural bioinformatics, molecular modeling and system bioinformatics methods.
Also Dmitrii has a wide experience in system administration, programming and data analysis

His most recent research is studying of the specific roles of single amino acid mutations in bacterial ẞ-lactamases (RSF funded project) and studying of antibody-ganglioside interactions  (RFBR grant).

In 2016 he joined Moscow Polytechnical University as an assistant professor in Bioinformatics.

Besides academical work Dmitrii developed and managed several contract research and educational projects for SSMU (Tomsk), FEFU (Vladivostok), Nearmedic LLC, AWT medicals LLC and carried out some joint molecular modeling projects for Visual Science studio:

http://visual-science.com/projects/zika/3d- model/

http://visual-science.com/projects/influenza/illustration/

Here at Skoltech Dmitrii is studying regulation of stem cells differentiation and inducing of pluripotency using mathematical modeling and network analysis.

Quantitative modeling of pluripotency gene networks

1. D. S. Shcherbinin and A. V. Veselovsky. Investigation of Interaction of Thrombin-Binding Aptamer with Thrombin and Prethrombin-2 by Simulation of Molecular Dynamics. // Biophysics, 2013, Vol. 58, No. 3, pp. 315–323
2. Sergey V. Stulov, Olga V. Mankevich, Roman A. Novikov b, Yaroslav V. Tkachev, Vladimir P. Timofeev, Nikita O. Dugin, Vladimir F. Pozdnev, Irina V. Fedyushkina, Dmitri Scherbinin , Alexander V. Veselovsky, Alexander Yu. Misharin. Synthesis and molecular modeling of (40R)- and (40S)- 40-substituted 20-{[(E)-androst-5-en-17-ylidene]-methyl}oxazolines // Steroids, 2013, Vol. 78, No 5, pp. 521–527
3.  V. R. Khayrullina1*, I. A. Taipov1, A. V. Veselovsky, D. S. Shcherbinin, and A.Gerchikov1. New Inhibitors of 5 Lipoxygenase Catalytic Activity Based on 2 (3Methylphenyl)propanoic Acid and 4 Substituted Morpholine Derivatives // Biochemistry (Moscow), 2014, Vol. 79, No. 4, pp. 376 384
4.  Alexey V. Kuzikov, Nikita O. Dugin, Sergey V. Stulov, Dmitry S. Shcherbinin, Maria S. Zharkova, Yaroslav V. Tkachev, Vladimir P. Timofeev, Alexander V. Veselovsky, Victoria V. Shumyantseva, and Alexander Y. Misharin. Novel oxazolinyl derivatives of pregna-5,17(20)-dieneas 17α-hydroxylase/17,20-lyase (cyp17a1) inhibitors // Steroids, 2014 Vol.88, pp. 66-71
5.  S. V. Stulov, N. O. Dugin, M. S. Zharkova, D. S. Shcherbinin, A. V. Kuzikov, V. V. Shumantseva, A. Yu. Misharin, and A. V. Veselovsky. Interaction of Novel Oxazoline Derivatives of 17(20)Epregna5,17(20)Diene with Cytochrome P450 // Biochemistry (Moscow) Supplement Series B: Biomedical Chemistry, 2015, Vol. 9, No. 2, pp. 114–120
6.  Dmitrii S. Shcherbinin, Oksana V. Gnedenko, Svetlana A. Khmeleva, Sergey A. Usanov, Andrei A. Gilep, Aliaksei V. Yantsevich, Tatsiana V. Shkel, Ivan V. Yushkevich, Sergey P. Radko, Alexis S. Ivanov, Alexander V. Veselovsky, Alexander I. Archakov. Computer-aided design of aptamers for cytochrome p450// J Struct Biol. 2015 2015 Vol. 191 (2), pp. 112–119. doi: 10.1016/j.jsb.2015.07.003
7. D.S. Shcherbinin, M.Yu. Rubtsova, V.G. Grigorenko, I.V. Uporov, A.V. Veselovsky, A.M. Egorov. Investigation the role of mutations m182t and q39k in structureof b-lactamase TEM-72 by molecular dynamics methods // Biomedical chemistry. 2016 vol. 62 (5), pp. 527-534.

Orekhovich Institute of Biomedical Chemistry, 2007-2013
Laboratory of Molecular Graphics and Drug Design.
PhD in mathematical biology and bioinformatics (Biological sciences, Higher Attestation Commission ID-03.01.09)

Moscow State University,  2002-2007
Department of Bioengineering and Bioinformatics.
Specialist (M.Sc.) in Bioengineering and Bioinformatics

Research interests:

  • Computer and Molecular modeling
  • Structural and System bioinformatics
  • Molecular dynamics
  • Molecular docking
  • Network analysis
  • Bioinformatics and biotechnology