Olga V. Kalinina
Ph.D. (math), Researcher

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Scientific interests

- Protein function & specificity
- Protein-ligand interactions
- Comparative genomics
- Bioinformatics of transmembrane proteins


2003-2006: post-graduate course at the Department of Bioengineering and Bioinformatics, MSU. Ph.D. in molecular biology. Ph.D. thesis: “Amino acids that determine specificity in large protein families”. Advisor: Mikhail S. Gelfand
1998-2003: Department of Mathematics and Mechanics, Moscow State University, Moscow, Russia. M.Sc. in mathematics, applied mathematics.

Research experience:

- September 2006 – December 2007: senior faculty member at the Department of Bioengineering and Bioinformatics, MSU
- February-June 2006: research scholar in Dr. Rob Russell’s group at EMBL (Heidelberg, Germany)
- October-December 2005: research scholar in Dr. Rob Russell’s group at EMBL (Heidelberg, Germany)


- Graduation with honors (magna cum laude) (2003)
- Prize for best presentation at the XI International Scientific Conference for Undergraduate and Graduate Students and Young Scientists (2004)
- Grants from International Soros Science Educational Program (2004, 2005)
- INTAS Fellowship Grant for Young Scientists (2005-2006)
- State Fellowship from the Government of the Russian Federation (2005-2006)
- EMBO long term fellowship (2008-2009)


Mazin P.V, Gelfand M.S, Mironov A.A, Rakhmaninova A.B, Rubinov A.R, Russell R.B, Kalinina O.V. An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies. Algorithms Mol Biol. 2010, 5: 29. PubMed  PDF

Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, Chen W, Wodke J, Guell M, Martinez S, Bourgeois R, Kuhner S, Raineri E, Letunic I, Kalinina O, Rode M, Herrmann R, Gutierrez-Gallego R, Russell R, Gavin A, Bork P, Serrano L. Impact of Genome Reduction on Bacterial Metabolism and Its Regulation. Science, 2009, 27: 1263-1268   PDF

Kalinina O.V, Gelfand M.S, Russell R.B. Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics. 2009, 10: 174. PubMed  PDF

Kalinina OV, Russell RB, Rakhmaninova AB, Gelfand MS. [Computational method for prediction of protein functional sites using specificity determinants.] Mol Biol (Mosk). 2007, 41(1):151-162. Russian. PubMed   PDF

 Permina EA, Kazakov AE, Kalinina OV, Gelfand MS. Comparative genomics of regulation of heavy metal resistance in Eubacteria. BMC Microbiology 2006, 6:49 PubMed  PDF

Kalinina OV, Gelfand MS. Amino acid residues that determine functional specificity of NADP- and NAD-dependent isocitrate and isopropylmalate dehydrogenases. Proteins. 2006, 64(4):1001-9 PubMed  PDF  Supplementary material

Devos D, Kalinina OV, Russell RB. Harry Potter and the structural biologist's (Key)stone. Genome Biol. 2006; 7(12):333. PubMed  PDF

Oparina NJ, Kalinina OV, Gelfand MS, Kisselev LL. Common and specific amino acid residues in the prokaryotic release factors RF1 and RF2: possible functional implications. Nucleic Acids Res. 2005. 33(16): 5226-5234. PubMed  PDF

Rakhmaninova AB, Kalinina OV, Minin VV. Discriminative sites in the conserved core of various annexin families from vertebrates. Annexins. 2004, 1(2): S137-S142

Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB. SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res. 2004, 32(Web Server issue):W424-8. PubMed   PDF

Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci. 2004, 13(2):443-56. PubMed   PDF

Kalinina O.V, Gelfand M.S, Mironov A.A, Rakhmaninova A.B. Amino acid residues forming specific contacts between subunits in tetramers of the membrane channel GlpF. Biophysics (Moscow). 2003, 48 Suppl. 1 S141-S145 PDF

Kalinina OV, Makeev VJ, Sutormin RA, Gelfand MS, Rakhmaninova AB. The channel in transporters is formed by residues that are rare in transmembrane helices. In Silico Biol. 2003, 3(1-2):197-204. PubMed