Laboratory of
System Biology and Bioinformatics

• "A terapeptide-based method for polyproline II-type secondary strcture prediction"
  Vlasov P.K., Vlasova A.V., Tumanyan V.G., Esipova N.G.
  Proteins, Vol. 61 (4), pp. 763-768.

• "Molecular modelling of disease-causing single-nucleotide polymorphisms in collagen"
  Milchevsky Ju.V., Ramensky V.E., Esipova N.G., Tumanyan V.G.,Zorov B.S.
  SAR and QSAR Environ Res., Vol. 12, pp. 383-399.
• "Bayesian approah to DNA segmentation into regions with different average nucleotide composition"
  Makeev V.Ju., Ramensky V.E., Gelfand, M.S., Roytberg, M.A., Tumanyan, V.G.
  Lectural Notes in Computer Science, Vol. 2066, Computational Biology, pp. 57–74.
• "Left-handed conformation of poly-L-proline II type in globular proteins. Sequence specificity"
  Vlasov P.K., Kilosanidze G.T., Ukrainskii D.L., Kuzmin A.V., Tumanyan V.G., Esipova N.G.
  Biophysics, Vol. 46, 3.
• "Prediction of deleterious human alleles"
  S.R.Sunyaev, V.E.Ramensky, I.Koch, W.C.Lathe III, A.S.Kondrashov, P.Bork.
  Hum Mol Genet., Vol.10, No 6, pp.591–597.

• "SNP frequencies in human genes: an excess of rare alleles and differing modes of selection"
  S.R.Sunyaev, W.C.Lathe III, V.E.Ramensky,P.Bork.
  Trends Genet, Vol. 16, No.8, pp.335–337
• "DNA segmentation through the Bayesian Approach"
  Ramensky V.E., Makeev V.Ju., Roytberg, M.A., Tumanyan, V.G.
  Journal of Computational Biology, 7, 215–231.
• "How do point amino acid substitutions affect the protein structure?"
  Ramenskii V.E., Vlasov P.K., Syunyaev Sh.R., Tumanyan V.G.
  Biophysics, Vol. 45, 220-227.
• "Towards a structural basis of human non-synonymous single nucleotide polymorphisms"
  S.R.Sunyaev, V.E.Ramensky, P.Bork.
  Trends Genet, Vol.16, No.5, pp. 198–200.

• "PSIC: Profile extraction from sequence alignments with position-specific counts of independent observations"
  Sunyaev Sh., Eisenhaber F., Rodchenkov I., Eisenhaber B., Tumanyan V., Kuznetsov Eu.
  Protein Eng., vol. 12, No. 5, pp. 387-394.
• "Amino acid composition of protein termini are biased in different manners"
  Berezovsky I.N., Kilosanidze G.T., Tumanyan V.G., Kisselev L.L.
  Protein Eng., vol. 12, No. 1, pp. 23-30.
• "Two-H-Bonded and One-H-bonded Structure Alterations in Collagen"
  Milchevsky Ju.V., Zhorov B.S., Esipova N.G., Tumanyan V.G.
  J. Biomol. Struct. & Dynamics, vol. 16, No. 4, pp. 977-988.
• "Hierarchy of the interaction energy distribution in the spatial structure of globular proteins and the problem of domain definition"
  Berezovsky I.N., Namiot V.A., Tumanyan V.G. and Esipova N.G.
  J. Biomol. Struct.&Dynamics, vol. 17, pp.133-15.

• "Conserved supersecondary structural motif in NAD-dependent dehydrogenases"
  Kutzenko A.S., Lamzin V.S., Popov V.O.
  FEBS Lett., vol. 423, No. 1, pp. 105-109.
• "Are knowledge-based potentials derived from protein-structure sets discriminative with respect to amino acid types"
  Sunyaev Sh.R., Eisenhaber F., Argos P., Kuznetsov Eu.N., Tumanyan V.G.
  Proteins, vol. 31, pp. 225-246.
• "Analysis of the position dependent amino acid probabilities and its application to the search for remote homologues"
  Sunyaev Sh.R., Rodchenkov I.V., Eisenhaber F., Kuznetsov Eu.N.
  RECOMB, vol. 98, pp. 258-265.
• "Distribution of aimed interactions in three-dimensional structures of globular proteins"
  Berezovsky I.N., Esipova N.G., Tumanyan V.G.
  Biofizika, vol. 43, No. 3, pp. 392-402.
• "Thermodynamic properties of lactate dehydrogenase from muscles of fishes adapted to defferent environmental temperatures"
  Danilenko A.N., Persikov A.V., Polosukhina E.S., Klyachko O.S., Esipova N.G., Ozernyuk N.D.
  Biofizika, vol.43, No1 , pp.26-30.

• "Protein-sequence-structure compatibility creteria in terms of statistical hypothesis testing"
  Sunyaev Sh., Kuznetsov Eu., Rodchenkov I., Tumanyan V.
  Protein Eng., vol. 10, No. 6, pp. 635-646.
• "G and T nucleotide contents show specie(?)-invariant negative correlation for all three codon positions"
  Frank G.K., Makeev V.Yu.
  J. Biomol. Struct. & Dynamics, vol. 14, No. 5, pp. 629-639.
• "Specie-invariant correlations in nucleotide content for different reading frame positions"
  Frank G.K., Makeev V.Ju.
  J.Biomol. Struct. and Dynam. 14, 629-639.
• "Representation of amino acid sequences in terms of interaction energy in protein globules"
  Berezovsky I.N., Tumanyan V.G., Esipova N.G.
  FEBS Lett., vol. 418, No. 1/2, pp. 43-46.
• "COOH-terminal decamers in proteins are non-random"
  Berezovsky I.N., Kilosanidze G.T., Tumanyan V.G., Kisselev L.
  FEBS Lett., vol. 404, No. 2/3, pp. 140-142.
• "The protein fold recognition as the statistical hypothesis testing and statistical analysis of residue environment parameters"
  Sunyaev Sh.R.
  Futura, vol. 12, pp. 233-236.
• "Fourier analysis of nucleotide sequences. Periodicity in promoter sequences of E. coli"
  Kutuzova G.I., Frank G.K., Makeev V.Yu., Esipova N.G., Polozov R.V.
  Biofizika, vol. 42, No. 2, pp. 354-362.

• "Search of periodicities in primary structure of biopolymers: a general Fourier approach"
  Makeev V.Yu., Tumanyan V.G.
  CABIOS, vol.12, No. 1, pp.49-54.
• "The statistic study of periodic regularities in sequences of human introns"
  Makeev V.Ju, Frank, G.K., Tumanyan V.G.
  Biofizika v.41, N1, 241-246.

• "The third nucleotide of the Gly coding triplet remembers the periodicity of the collagen chain"
  Makeev V.Yu., Tumanyan V.G., Esipova N.G.
  FEBS Lettr., vol.336, No 1, pp.33-36.