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  1. Article ; Online: Analysis to determine the effect of mutations on binding to small chemical molecules.

    Koshlan, T V / Kulikov, K G

    Journal of bioinformatics and computational biology

    2022  Volume 20, Issue 2, Page(s) 2240003

    Abstract: In this paper, the authors present and describe, in detail, an original software-implemented numerical methodology used to determine the effect of mutations on binding to small chemical molecules, on the example of gefitinib, AMPPNP, CO-1686, ASP8273, ... ...

    Abstract In this paper, the authors present and describe, in detail, an original software-implemented numerical methodology used to determine the effect of mutations on binding to small chemical molecules, on the example of gefitinib, AMPPNP, CO-1686, ASP8273, erlotinib binding with EGFR protein, and imatinib binding with PPARgamma. Furthermore, the developed numerical approach makes it possible to determine the stability of a molecular complex, which consists of a protein and a small chemical molecule. The description of the software package that implements the presented algorithm is given in the website: https://binomlabs.com/.
    MeSH term(s) Carcinoma, Non-Small-Cell Lung/genetics ; ErbB Receptors/genetics ; Humans ; Lung Neoplasms/genetics ; Mutation ; Quinazolines
    Chemical Substances Quinazolines ; ErbB Receptors (EC 2.7.10.1)
    Language English
    Publishing date 2022-04-14
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2115015-1
    ISSN 1757-6334 ; 0219-7200
    ISSN (online) 1757-6334
    ISSN 0219-7200
    DOI 10.1142/S0219720022400030
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Modeling the impact of point mutations on the stability of proteins.

    Kulikov, K G / Koshlan, T V

    Journal of bioinformatics and computational biology

    2020  Volume 18, Issue 4, Page(s) 2050019

    Abstract: A new method has been introduced which allows us to determine the stability of protein complexes with point changes of amino acid residues that also take into account the three-dimensional structure of the complex. This formulated and proven theorem is ... ...

    Abstract A new method has been introduced which allows us to determine the stability of protein complexes with point changes of amino acid residues that also take into account the three-dimensional structure of the complex. This formulated and proven theorem is aimed at determining the criterion for the stability of protein molecules. The algorithm and software package were developed for analyzing protein interactions, taking into account their three-dimensional structure from the PDB database.
    MeSH term(s) Algorithms ; Amino Acid Substitution ; Computational Biology/methods ; Entropy ; Point Mutation ; Protein Domains ; Protein Stability ; Proteins/chemistry ; Proteins/genetics ; Proto-Oncogene Proteins c-bcl-2/chemistry ; Proto-Oncogene Proteins c-bcl-2/genetics ; Proto-Oncogene Proteins c-bcl-2/metabolism ; bcl-2-Associated X Protein/chemistry ; bcl-2-Associated X Protein/metabolism
    Chemical Substances Proteins ; Proto-Oncogene Proteins c-bcl-2 ; bcl-2-Associated X Protein
    Language English
    Publishing date 2020-07-10
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2115015-1
    ISSN 1757-6334 ; 0219-7200
    ISSN (online) 1757-6334
    ISSN 0219-7200
    DOI 10.1142/S0219720020500195
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: An innovative method for the selection of inhibitors of the viral spike-glycoprotein of the SARS-CoV.

    Koshlan, T V / Kulikov, K G

    Journal of bioinformatics and computational biology

    2020  Volume 19, Issue 1, Page(s) 2050043

    Abstract: This paper has developed and described a detailed method for selecting inhibitors based on modified natural peptides for the SARS-CoV BJ01 spike-glycoprotein. The selection of inhibitors is carried out by increasing the affinity of the peptide to the ... ...

    Abstract This paper has developed and described a detailed method for selecting inhibitors based on modified natural peptides for the SARS-CoV BJ01 spike-glycoprotein. The selection of inhibitors is carried out by increasing the affinity of the peptide to the active center of the protein. This paper also provides a step-by-step algorithm for analyzing the affinity of protein interactions and presents an analysis of energy interactions between the active center of a protein and the wild-type peptide interacting with it, taking into account modifications of the latter. A description of the software package that implements the presented algorithm is given on the website https://binomlabs.com/covid19.
    MeSH term(s) Algorithms ; Amino Acid Substitution ; Antiviral Agents/pharmacology ; Catalytic Domain ; Drug Evaluation, Preclinical/methods ; Entropy ; Protein Interaction Domains and Motifs/genetics ; Proteins/chemistry ; Proteins/genetics ; Proteins/metabolism ; Proteins/pharmacology ; Software ; Spike Glycoprotein, Coronavirus/antagonists & inhibitors ; Spike Glycoprotein, Coronavirus/chemistry ; Spike Glycoprotein, Coronavirus/metabolism
    Chemical Substances Antiviral Agents ; Proteins ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
    Keywords covid19
    Language English
    Publishing date 2020-11-19
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2115015-1
    ISSN 1757-6334 ; 0219-7200
    ISSN (online) 1757-6334
    ISSN 0219-7200
    DOI 10.1142/S0219720020500432
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Letal'noe i mutagennoe deĭstvie izlucheniĭ s raznoĭ LPE na kletki mlekopitaiushchikh.

    Shmakova, N L / Krasavin, E A / Govorun, R D / Fadeeva, T A / Koshlan', I V

    Radiatsionnaia biologiia, radioecologiia

    1997  Volume 37, Issue 2, Page(s) 213–219

    Abstract: Inactivation and induction of mutations in the HGPRT locus in Chinese hamster cells after irradiation with accelerated heavy ions in the LET range of 20 to 367 keV/micron were studied. In both cases, inactivation and induction of mutations, the LET ... ...

    Title translation The lethal and mutagenic actions of radiations with different LETs on mammalian cells.
    Abstract Inactivation and induction of mutations in the HGPRT locus in Chinese hamster cells after irradiation with accelerated heavy ions in the LET range of 20 to 367 keV/micron were studied. In both cases, inactivation and induction of mutations, the LET dependence of RBE is described by a curve with a local maximum in the range of 80 to 100 keV/micron. The maximum RBE value for the mutagenic action is almost twice as high as that for inactivation. However, the RBE coefficients of the mutation induction criterion for a certain level of cell-survival is lower significantly and tend to decrease with an increase in inactivation. The obtained data show that the mutagenic effects, induction of chromosome aberrations, and deaths have their origins in the same kind of primary damages, i.e., double-strand breaks of DNA.
    MeSH term(s) Animals ; Cell Death/radiation effects ; Cells, Cultured ; Chromosome Aberrations ; Cricetinae ; Cricetulus ; Dose-Response Relationship, Radiation ; Fibroblasts/radiation effects ; Gamma Rays ; Hypoxanthine Phosphoribosyltransferase/genetics ; Hypoxanthine Phosphoribosyltransferase/radiation effects ; Linear Energy Transfer ; Mutation ; Particle Accelerators ; Time Factors
    Chemical Substances Hypoxanthine Phosphoribosyltransferase (EC 2.4.2.8)
    Language Russian
    Publishing date 1997-03
    Publishing country Russia (Federation)
    Document type Comparative Study ; English Abstract ; Journal Article
    ZDB-ID 1176728-5
    ISSN 0869-8031
    ISSN 0869-8031
    Database MEDical Literature Analysis and Retrieval System OnLINE

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