Search Results - "Tumanyan, Vladimir G"

Omnipresence of the polyproline II helix in fibrous and globular proteins by Esipova, Natalia G, Tumanyan, Vladimir G

“…[Display omitted] •The polyproline II helix is omnipresent.•Role of proline in stability of PPII helix and its interactions.•Specific mechanisms work in PPII…”
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Core Promoter Regions of Antisense and Long Intergenic Non-Coding RNAs by Savina, Ekaterina A, Shumilina, Tatiana G, Tumanyan, Vladimir G, Anashkina, Anastasia A, Il'icheva, Irina A

“…RNA polymerase II (POL II) is responsible for the transcription of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). Previously, we have shown the…”
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Structural coordinates: A novel approach to predict protein backbone conformation by Milchevskaya, Vladislava, Nikitin, Alexei M, Lukshin, Sergey A, Filatov, Ivan V, Kravatsky, Yuri V, Tumanyan, Vladimir G, Esipova, Natalia G, Milchevskiy, Yury V

“…Local protein structure is usually described via classifying each peptide to a unique class from a set of pre-defined structures. These classifications may…”
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Comparative analysis of the quality of a global algorithm and a local algorithm for alignment of two sequences by Polyanovsky, Valery O, Roytberg, Mikhail A, Tumanyan, Vladimir G

“…Algorithms of sequence alignment are the key instruments for computer-assisted studies of biopolymers. Obviously, it is important to take into account the…”
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Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations by Torshin, Ivan Yu, Namiot, Vladimir A., Esipova, Natalia G., Tumanyan, Vladimir G.

“…The fundamental criteria of the quality of molecular dynamics (MD) simulation represent a pivotal challenge, especially in the case of MD simulations of large…”
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Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II′ region of the Ramachandran plot by Torshin, Ivan Yu, Esipova, Natalya G., Tumanyan, Vladimir G.

“…The structure of the SH3 domain of α-spectrin (PDB code 1SHG) features Asn47 in the II′ area of the Ramachandran plot, which as a rule admits only glycine…”
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Structural attributes of nucleotide sequences in promoter regions of supercoiling-sensitive genes: How to relate microarray expression data with genomic sequences by Kravatskaya, Galina I., Chechetkin, Vladimir R., Kravatsky, Yury V., Tumanyan, Vladimir G.

“…The level of supercoiling in the chromosome can affect gene expression. To clarify the basis of supercoiling sensitivity, we analyzed the structural features…”
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A Novel Model System for Design of Biomaterials Based on Recombinant Analogs of Spider Silk Proteins by Bogush, Vladimir G., Sokolova, Olga S., Davydova, Lyubov I., Klinov, Dmitri V., Sidoruk, Konstantin V., Esipova, Natalya G., Neretina, Tatyana V., Orchanskyi, Igor A., Makeev, Vsevolod Yu, Tumanyan, Vladimir G., Shaitan, Konstantin V., Debabov, Vladimir G., Kirpichnikov, Mikhail P.

“…Spider dragline silk possesses impressive mechanical and biochemical properties. It is synthesized by a couple of major ampullate glands in spiders and…”
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Reconstruction of genuine pair-wise sequence alignment by Polyanovsky, Valery, Roytberg, Mikhail A, Tumanyan, Vladimir G

“…In many applications, the algorithmically obtained alignment ideally should restore the "golden standard" (GS) alignment, which superimposes positions…”
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A tetrapeptide-based method for polyproline II-type secondary structure prediction by Vlasov, Peter K., Vlasova, Anna V., Tumanyan, Vladimir G., Esipova, Natalia G.

“…We describe a new method for polyproline II‐type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from…”
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Analysis of forces that determine helix formation in α‐proteins by Kilosanidze, Gelena T., Kutsenko, Alexey S., Esipova, Natalia G., Tumanyan, Vladimir G.

“…A model for prediction of α‐helical regions in amino acid sequences has been tested on the mainly‐α protein structure class. The modeling represents the…”
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Study and Prediction of Secondary Structure for Membrane Proteins by Amirova, Svetlana R., Milchevsky, Juri V., Filatov, Ivan V., Esipova, Natalia G., Tumanyan, Vladimir G.

“…In this paper we present a novel approach to membrane protein secondary structure prediction based on the statistical stepwise discriminant analysis method. A…”
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Use of molecular mechanics for secondary structure prediction. Is it possible to reveal α-helix? by Kilosanidze, Gelena T, Kutsenko, Alexey S, Esipova, Natalia G, Tumanyan, Vladimir G

“…A new approach to predicting protein standard conformations is suggested. The idea consists in modeling by molecular mechanics tools a continuous α-helical…”
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Representation of amino acid sequences in terms of interaction energy in protein globules by Berezovsky, Igor N, Tumanyan, Vladimir G, Esipova, Natalia G

“…We suggest a new simple approach for comparing the primary structure of proteins and their spatial structure. It relies on the one-to-one correspondence…”
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Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software by Ramensky, Vasily E., Makeev, Vsevolod Ju, Roytberg, Mikhail A., Tumanyan, Vladimir G.

“…We present a software system BASIO that allows one to segment a sequence into regions with homogeneous nucleotide composition at a desired length scale. The…”
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COOH-terminal decamers in proteins are non-random by Berezovsky, Igor N, Kilosanidze, Gelena T, Tumanyan, Vladimir G, Kisselev, Lev

“…We have undertaken an exhaustive statistical analysis of the amino acid sequences at the carboxyl-terminal (C) ends of proteins. The composition of the…”
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PSIC: profile extraction from sequence alignments with position-specific counts of independent observations by Sunyaev, Shamil R., Eisenhaber, Frank, Rodchenkov, Igor V., Eisenhaber, Birgit, Tumanyan, Vladimir G., Kuznetsov, Eugene N.

“…Sequence weighting techniques are aimed at balancing redundant observed information from subsets of similar sequences in multiple alignments. Traditional…”
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Amino acid composition of protein termini are biased in different manners by Berezovsky, Igor N., Kilosanidze, Gelena T., Tumanyan, Vladimir G., Kisselev, Lev L.

“…An exhaustive statistical analysis of the amino acid sequences at the carboxyl (C) and amino (N) termini of proteins and of coding nucleic acid sequences at…”
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Are knowledge-based potentials derived from protein structure sets discriminative with respect to amino acid types? by Sunyaev, Shamil R., Eisenhaber, Frank, Argos, Patrick, Kuznetsov, Eugene N., Tumanyan, Vladimir G.

“…The parametric description of residue environments through solvent accessibility, backbone conformation, or pairwise residue–residue distances is the key to…”
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Hierarchy of the Interaction Energy Distribution in the Spatial Structure of Globular Proteins and the Problem of Domain Definition by Berezovsky, Igor N., Namiot, Vladimir A., Tumanyan, Vladimir G., Esipova, Natalia G.

“…An algorithm for determining of protein domain structure is proposed. Domain structures resulted from the algorithm application have been obtained and compared…”
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