IBCh positions

2019–2025

Senior research fellow

Laboratory of protein engineering

Titles

	Doctor of Philosophy (Physico-mathematical sciences)

Scientific results

1. Gabrielian A.E., Nekrasov A.N., Kirpichnikov M.P.

"Comparison of the predictive abilities of different methods based on information theory: searching for receptor-binding sites"

Biomed. Sci. (1991) vol. 2(5), pp. 481-484.

PMID: 1840836

 

2. Nekrasov A.N., Stepanov A.V., Timofeev V.P.

"The features of the spatial structure of the gramicidine A-cesium complex"

FEBS Lett. (1995) vol. 371(1), pp. 35-38.

DOI: 10.1016/0014-5793(95)00800-o

 

3. Nekrasov A.N., Mikhaleva I.I.

"Cyclo(-GLY-DSIP), A cyclic analog of the delta-sleep-inducing peptide: computer simulation of spatial structure involving NMR data"

Biochem. Mol. Biol. Int. (1996) vol. 38(4), pp. 739-745.

PMID: 8728103

 

4. Nekrasov A.N., Lexikova E.E., Karelin A.A.

"Modeling of in vivo proteolytic degradation of hemoglobin" J. Biomol. Struct. Dyn. (1997) vol. 15(2), pp. 393-399.

DOI: 10.1080/07391102.1997.10508201

 

5. Rogov S.I., Nekrasov A.N.

"A numerical measure of amino acid residues similarity based on the analysis of their surroundings in natural protein sequences" Protein. Eng. (2001) vol. 14(7), pp. 459-463.

DOI: 10.1093/protein/14.7.459   Q1

 

6. Nekrasov A.N.

"Entropy of protein sequences: an integral approach"

J. Biomol. Struct. Dyn. (2002) vol. 20(1), pp. 87-92.

DOI: 10.1080/07391102.2002.10506825

 

7. Nekrasov A.N.

"Analysis of the information structure of protein sequences: a new method for analyzing the domain organization of proteins"

J. Biomol. Struct. Dyn. (2004) vol. 21(5), pp. 615-624.

DOI: 10.1080/07391102.2004.10506952

 

8. Svirshchevskaya E., Alekseeva L., Marchenko A., Benevolenskii S., Berzhec V.M., Nekrasov A.

"Selection of cryptic B-cell epitopes using informational analysis of protein sequences"

J. Bioinform. Comput. Biol. (2006) vol. 4(2), pp. 389-402.  

DOI: 10.1142/s0219720006002053.

 

9. Alekseeva L., Nekrasov A., Marchenko A., Shevchenko M., Benevolenskii S., Sapozhnikov A., Kurup V.P., Svirshchevskaya E.

"Cryptic B-cell epitope identification through informational analysis of protein sequences"

Vaccine (2007) vol. 25(14), pp. 2688-2697.

DOI: 10.1016/j.vaccine.2006.07.003

 

10. Nekrasov A.N., Radchenko V.V., Shuvaeva T.M., Novoselov V.I., Fesenko E.E., Lipkin V.M.

"The Novel Approach to the Protein Design: Active Truncated Forms of Human 1-CYS Peroxiredoxin"

J. Biomol. Struct. Dyn. (2007) vol. 24(5), pp. 455-462.

DOI: 10.1080/07391102.2007.10507133 

 

11. Anisimova V.E., Shcheglov A.S., Bogdanova E.A., Rebrikov D.V., Nekrasov A.N., Barsova E.V., Shagin D.A., Lukyanov S.A.

"Is crab duplex-specific nuclease a member of the Serratia family of non-specific nucleases?"

Gene (2008) vol. 418(1-2), pp. 41-48. 

Epub 2008 Apr 16.

DOI: 10.1016/j.gene.2008.04.005.   Q2

 

12. Nekrasov A.N., Zinchenko A.A.

"Hydrolases: The Correlation between Informational Structure and the Catalytic Centers Organization"

J. Biomol. Struct. Dyn. (2008) vol. 25(5), pp. 553-562.

DOI: 10.1080/07391102.2008.10507202 

 

13. Briers Y., Miroshnikov K., Chertkov O., Nekrasov A., Mesyanzhinov V., Volckaert G., Lavigne R.

“The structural peptidoglycan hydrolase gp181 of bacteriophage phiKZ”

Biochem Biophys Res Commun. (2008) vol. 374(4), pp.747-751.

Epub 2008 Jul 29.

DOI: 10.1016/j.bbrc.2008.07.102.  

 

14. Nekrasov A.N., Petrovskaya L.E., Toporova V.A., Kryukova E.A., Rodina A.V., Moskaleva E.Y., Kirpichnikov M.P. "Design of a novel interleukin-13 antagonist from analysis of informational structure" Biochemistry (Mosc). (2009) vol. 74(4), pp. 399-405.

DOI: 10.1134/s0006297909040075  

 

15. Nekrasov A.N., Zinchenko A.А.

"Structural Features of the Interfaces in Enzyme-Inhibitor Complexes"

J. Biomol. Struct. Dyn. (2010) vol. 28(1), pp. 85-96.

DOI: 10.1080/07391102.2010.10507345

 

16. Shingarova L.N., Petrovskaia L.E., Nekrasov A.N., Kriukova E.A., Boldyreva E.F., Iakimov S.A., Gur'ianova S.V., Dolgikh D.A., Kirpichnikov M.P.

"Expression and Properties of Human TNF Peptide Fragments"

Russ. J. Bioorganic Chem. (2010), vol. 36, pp. 327–336,

DOI: 10.1134/s1068162010030040

 

17. Kobylyansky A.G., Nekrasov A.N., Kozlova V.I., Sandin M.Y., Alikhanov B.A., Demkin V.V.

"Detection of new epitopes of antibodies to filaggrin in filaggrin protein molecule"

Bull. Exp. Biol. Med. (2011) vol. 151(5), pp. 615-618.

DOI: 10.1371/journal.pone.0168542   Q3

 

18. Ostroverkhova T.V., Chertkova R.V., Nekrasov A.N., Dolgikh D.A., Kirpichnikov M.P.

"Design of Mutant Variants of Horse Cytochrome C by Analysis of Informational Structure Method and Testing its Biological Activity"

Moscow University Biological Sciences Bulletin (2011), vol. 66(2), pp. 65–67.   

https://doi.org/10.3103/S0096392511020064

 

19. Anashkina A.A., Nekrasov A.N.

"The method for identification of hierarchical organization of protein sequences"  

Russian Journal of Numerical Analysis and Mathematical Modelling (2014) vol. 29(5), pp. 266–273.

DOI: 10.1515/rnam-2014-0021   Q2

 

20. Mikhailova A.G., Nekrasov A.N., Zinchenko A.A., Rakitina T.V., Korzhenevsky D.A., Lipkin A.V., Razguljaeva O.A., Ovchinnikova M.V., Gorlenko V.A., Rumsh L.D.

"Truncated variants of Serratia proteamaculans oligopeptidase B having different activities"

Biochemistry (Moscow) (2015) 80(10), pp.1331-1343.

DOI: 10.1134/S0006297915100156.

 

21. Chertkova R.V., Brazhe N.A., Bryantseva T.V., Nekrasov A.N., Dolgikh D.A., Yusipovich A.I., Sosnovtseva O., Maksimov G.V., Rubin A.B., Kirpichnikov M.P.

"New insight into the mechanism of mitochondrial cytochrome c function"

PLoS One (2017) vol. 12(5): e0178280. eCollection 2017. 

DOI: 10.1371/journal.pone.0178280.

 

22. Alexei N. Nekrasov, Ludmila G. Alekseeva, Rudolf А. Pogosyan, Dmitry A. Dolgikh, M.P. Kirpichnikov, Alexandre G. de Brevern, Anastasia A. Anashkina

"A minimum set of stable blocks for rational design of polypeptide chains"

Biochimie (2019), vol. 160, pp. 88-92.

DOI: 10.1016/j.biochi.2019.02.006

 

23. A.I. Mikhalskii, I.V. Petrov, 1 V.V. Tsurko, A.A. Anashkina, A.N. Nekrasov

“Application of mutual information estimation 3 for predicting the structural stability of pentapeptides”

Russian Journal of Numerical Analysis and Mathematical Modelling (2020) vol.35, No.5, pp.263-271.

doi.org/10.1515/rnam-2020-0022

 

24 A.N. Nekrasov, Y.P. Kozmin, S.V. Kozyrev, R.H. Ziganshin, A.G. de Brevern, A.A. Anashkina

"Hierarchical Structure of Protein Sequence"

Int. J. Mol. Sci. (2021) vol.22, p.8339.

https://doi.org/10.3390/ ijms22158339

 

25. R.V. Chertkova1, T.V. Bryantseva1, N.A. Brazhe, K.S. Kudryashova, V.V. Revin , A.N. Nekrasov, A.I. Yusipovich, A.R. Brazhe, A.B. Rubin, D.A. Dolgikh, M.P. Kirpichnikov, G.V. Maksimov

"Aminoacid Substitutions in the non-ordered Ω-loop 70-85 Affect Electron transfer Function and Secondary Structure of Mitochondrial Cytochrome c"

Crystals (2021) vol.11, 973.

https://doi.org/10.3390/cryst 11080973

 

26. A.N. Nekrasov, А.А. Anashkina, А.А. Zinchenko "A new paradigm of protein structural organization" Proceedings of the 2nd International Conference "Theoretical Approaches to BioInformation Systems" (TABIS 2013) Institute of Physics Belgrade, SERBIA 2014, pp. 1-24, ISBN 978-86-82441-40-3.

https://www.researchgate.net/profile/Alexei-Nekrasov/publication/270684947_A_New_Paradigm_of_Protein_Structural_Organization/links/54b285da0cf220c63cd25c21/A-New-Paradigm-of-Protein-Structural-Organization.pdf#page=15