Fedonin G.G., Rakhmaninova A.B., Korostelev Iu D., Laikova O.N., Gel'fand M.S. [Machine learning study of DNA binding by transcription factors from the LacI family]. Mol Biol (Mosk) 2011 45(4): 724-737. Russian. PubMed  PDF

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

Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev Y.D, Rakhmaninova A.B, Gelfand M.S, Rodionov D.A, Raffaelli N, Zhang H. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51. PubMed  PDF

Gelfand MS, Kazakov AE, Korostelev YD, Laikova ON, Mironov AA, Rakhmaninova AB, Ravcheev DA, Rodionov DA, Vitreschak AG. Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4

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

Ravcheev DA, Rakhmaninova AB, Mironov AA, Gel'fand MS. [Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria]. Mol Biol (Mosk). 2005, 39(5):832-46. Russian. 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

Sutormin RA, Rakhmaninova AB, Gelfand MS. BATMAS30: amino acid substitution matrix for alignment of bacterial transporters. Proteins. 2003, 51(1):85-95. PubMed   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

Kalinina OV, Gelfand MS, Mironov AA, Rakhmaninova AB. Amino acid residues forming specific contacts between subunits in tetramers of the membrane channel GlpF. Biophysics (Moscow). 2003, 48 Suppl. 1 S141-S145

Ravcheev DA, Gel'fand MS, Mironov AA, Rakhmaninova AB. [Purine regulon of gamma-proteobacteria: a detailed description]. Genetika. 2002, 38(9):1203-14. Russian. PubMed   PDF

Sadovskaya NS, Sutormin RA, Rakhmaninova AB, Gelfand MS. The comparative analysis of programs for prediction of transmembrane segments in transmembrane proteins. Information Processes. 2002, 2(1): 96-99. [The article in Russian] PDF

Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria. J Mol Microbiol Biotechnol. 2001, 3(2):319-24. PubMed   PDF

Rakhmaninova AB, Mironov AA. [Change in entropy of the free polypeptide chain during formation of hydrogen bonds]. Mol Biol (Mosk). 2001, 35(3):451-61. Russian. PubMed

Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Mol Microbiol. 2000, 38(4):673-83. PubMed   PDF

Grigor'ev IV, Mironov AA, Rakhmaninova AB. [Refinement of helix boundaries in alpha-helical globular proteins]. Mol Biol (Mosk). 1999, 33(2):242-51. Russian. PubMed

Grigoriev IV, Rakhmaninova AB, Mironov AA. Simulated annealing for alpha-helical protein folding: searches in vicinity of the "molten globule" state. J Biomol Struct Dyn. 1998, 16(1):115-22. PubMed

Grigor'ev IV, Rakhmaninova AB, Mironov AA. [Modeling of folding of alpha-helical proteins with known secondary structure] Mol Biol (Mosk). 1998, 32(3):515-20. Russian. PubMed

Grigor'ev IV, Derebianko SV, Rakhmaninova AB, Mironov AA. [The assessment of a free energy of globular proteins' loops] Mol Biol (Mosk). 1997, 31(6):1064-70. Russian. PubMed

Grigoriev IV, Mironov AA, Rakhmaninova AB. Interhelical contacts determining the architecture of alpha-helical globular proteins. J Biomol Struct Dyn. 1994, 12(3):559-72. PubMed

Bakalkin GY, Rakhmaninova AB, Akparov VK, Volodin AA, Ovchinnikov VV, Sarkisyan RA. Amino acid sequence pattern in the regulatory peptides. Int J Pept Protein Res. 1991, 38(6):505-10. PubMed

Bakalkin GIa, Rakhmaninova AB, Sarkisian RA. [Regulatory peptides consisting of less than 20 amino acid residues are statistically periodical]. Dokl Akad Nauk SSSR. 1986, 289(3):721-724. Russian. PubMed

Tropsha AE, Rakhmaninova AB, Iaguzhinskii LS. Bioorg Khim. [Configuration and properties of a binding site for thyroid hormones on a specific receptor] Bioorg Khim., 1984, 10(4):483-92. Russian. PubMed

Kostava VT, Sharyshev AA, Rakhmaninova AB, Votiakova TV, Evtodienko IuV. [Induction of ion transport coupled to oxidative reactions in the membranes of mitochondria and liposomes]. Biofizika. 1979, 24(2):230-234. Russian. PubMed

Rakhmaninova AB, Khavkin EE, Yaguzhinksij LS. [Model for auxin receptor]. Biokhimiia. 1978, 43(5):806-823. Russian. PubMed

Yaguzhinsky LS, Boguslavsky LI, Volkov AG, Rakhmaninova AB. Synthesis of ATP coupled with action of membrane protonic pumps at the octane-water interface. Nature. 1976, 259(5543):494-496. PubMed

Iaguzhinskii LS, Boguslavslii LI, Volkov AG, Rakhmaninova AB. [ATP synthesis connected with the functioning of membrane proton pumps at the octane/water interface]. Dokl Akad Nauk SSSR. 1975, 221(6):1465-1468. Russian. PubMed