Výsledky vyhledávání - "Iu N, Vorob'ev"

[Molecular dynamics method for proteins with ionization-conformation coupling and equilibrium titration]

Autor: Iu N, Vorob'ev

Publikováno v: Molekuliarnaia biologiia. 45(2)

A new realization of the constant-pH molecular dynamics simulation method is proposed. Molecular dynamics simulation is performed for a protein in the most probable ionization microstate of the current conformation taking into account the potential o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::fdf6eb453460dd6b01b96afdac2c1f9c
https://pubmed.ncbi.nlm.nih.gov/21634122

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[GUI-BioPASED program for molecular dynamics modelling of biopolymers with a graphical user interface]

Autor: A V, Popov, Iu N, Vorob'ev

Publikováno v: Molekuliarnaia biologiia. 44(4)

There are several software packages that allow the user to model main types of biopolymers with molecular dynamics methods. However, the work with most of these packages is quite complicated, especially for non-experts in computational structural bio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::5a9fb4b948604872a69e06c9d6d3390d
https://pubmed.ncbi.nlm.nih.gov/20873234

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[Molecular modeling of positioning of human release factor eRF1 relative to mRNA stop-codon explains a proximity of the eRF1 C-domain to stop-codon in ribosomal complex]

Autor: Iu N, Vorob'ev, L L, Kiselev

Publikováno v: Molekuliarnaia biologiia. 42(2)

A properties of atomic models of structure of eukaryotic triple complex eRF1 . mRNA . tRNAPhe containing human class-1 polypeptide release factor eRF1 at the A-site of human 80S ribosome, mRNA and P-site tRNAPhe, obtained before, are considered. The

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::2504412cf987ecffeeb6e1a5954247cd
https://pubmed.ncbi.nlm.nih.gov/18610843

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[Molecular modeling of structure of eukaryotic ribosomal translation termination complex]

Autor: Iu N, Vorob'ev, L L, Kiselev

Publikováno v: Molekuliarnaia biologiia. 41(1)

Models of atomic structure of eukaryotic translation termination complex containing mRNA, P-site tRNAPhe, human class-1 polypeptide release factor eRF1 and 80S ribosome were constructed. The method of computational modeling was applied. The modeling

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::81e0a4186cdbaf5a0e54c354bd97a61d
https://pubmed.ncbi.nlm.nih.gov/17380897

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[Modeling of the mechanism of interactions of oligonucleotides with 3'-end of the yeast tRNA(Phe)]

Autor: Iu N, Vorob'ev

Publikováno v: Molekuliarnaia biologiia. 39(5)

Three dimensional atomic models of complexes between 10-, 15-mer long oligonucleotides and east tRNAPhe have been calculated. It has been found that the fast-forming primary complexes are the major groove complexes with the coaxial acceptor- and T-st

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::cfd9468fd29f7eb99d80fdfc988565b8
https://pubmed.ncbi.nlm.nih.gov/16240722

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[Study of the spatial structure of the product of intracomplex alkylation of the octanucleotide pd(TGTTTGGC) by 4-(N-methyl-N-(2-chloroethyl) amino)benzyl-5'-phosphamide derivative of the heptanucleotide pd(CCAAACA) in an aqueous solution by two-dimensional 1H-NMR spectroscopy and constrained molecular mechanics]

Autor: L A, Gorenshteĭn, E V, Bichenkova, Iu N, Vorob'ev, A V, Lebedev

Publikováno v: Bioorganicheskaia khimiia. 21(6)

Using one- and two-dimensional 1H NMR spectroscopy (400 MHz), a detailed study of the spatial structure of the covalent adduct, a product of the intracomplex alkylation of octanucleotide pd[TGTTTGGC] by the 4-[N-methyl-N-(2-chloroethyl)amino]benzyl-5

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::d4445a91b24817543ea0f705e9b66b05
https://pubmed.ncbi.nlm.nih.gov/7661868

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[Study of the spatial structure of the duplex (Phn-NH(CH2)NH)pd(CCAAACA).pd(TGTTTGGC) with covalently bound 10-(2-hydroxyethyl)phenazine by in aqueous solution by 2D-(1)H-NMR and by limited molecular mechanics]

Autor: E V, Bichenkova, L A, Gorenshteĭn, Iu N, Vorob'ev, E Iu, Tenne, V F, Zarytova, E M, Ivanova, T V, Mal'tseva, A V, Lebedev

Publikováno v: Bioorganicheskaia khimiia. 18(7)

Detailed investigation of the spatial structure of duplex (Phn-NH(CH2)2NH) x pd(CCAAACA).pd(TGTTTGGC) having a covalently linked N-(2-hydroxyethyl)-phenazine in aqueous solution was continued by means of one- and two-dimensional 1H-NMR spectroscopy.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::a39c79c413727a8106c47842f0efa7d8
https://pubmed.ncbi.nlm.nih.gov/1445427

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[Modification of nucleic acids by reactive oligonucleotide derivatives having a 5'-terminal nitrogen yperite residue, covalently bound with linkers of varying length. Conformation dynamics of group reactivity in complementary complexes]

Autor: N B, Bulychev, Iu N, Vorob'ev, A A, Koshkin, G V, Shishkin

Publikováno v: Bioorganicheskaia khimiia. 17(6)

By optimizing the length of a linker bearing 5'-terminal alkylating 4-[methyl-(2-chloroethyl)amino]benzylphosphoramide residue, a reactive oligodeoxyribonucleotide derivative has been constructed with an optimal ability to alkylate nucleic bases in a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::18a09bd8a310d3b9ba4d42237c15bf43
https://pubmed.ncbi.nlm.nih.gov/1776963

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[Study of the structural-energy aspects of complementary-addressed modifications of nucleic acids by reactive oligonucleotide derivatives having a 4-[N-methyl-N-(2-chloroethyl)amino[benzylidene group at the 3'end by a molecular mechanics method]

Autor: Iu N, Vorob'ev

Publikováno v: Bioorganicheskaia khimiia. 17(2)

Calculations of probabilities of the complementary addressed modification of a target nucleic acid by derivatives of oligonucleotides carrying a 4-[N-(2-chloroethyl)-N-methyl]aminobenzylidene group attached to the 3'-end (3'-BDO) have been made. The

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::4d0557b5c5050a1c2c87eb843104b20b
https://pubmed.ncbi.nlm.nih.gov/1863281

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[Study of the structural-energy aspects of complementary-addressed modifications of nucleic acid with reactive 4-]N-methyl-N-(2-chloroethyl)-amino]benzyl-3'- or 5'-phosphamide oligonucleotide derivatives by a molecular mechanics method]

Autor: Iu N, Vorob'ev

Publikováno v: Bioorganicheskaia khimiia. 17(2)

Calculations of probabilities of the complementary addressed modification of target NA by 3'- or 5'-reactive derivatives of oligonucleotides carrying a 4-[N-(2-chloroethyl)-N-methyl]aminobenzyl group attached to the 3'- or 5'-terminal phosphates thro

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::68161d741b1c9ae8df47d383bb3136c9
https://pubmed.ncbi.nlm.nih.gov/1863280

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