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  1. Article ; Online: Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric

    Barozi, Victor / Musyoka, Thommas Mutemi / Sheik Amamuddy, Olivier / Tastan Bishop, Özlem

    ACS omega

    2022  Volume 7, Issue 15, Page(s) 13313–13332

    Abstract: Resistance mutations ... ...

    Abstract Resistance mutations in
    Language English
    Publishing date 2022-04-07
    Publishing country United States
    Document type Journal Article
    ISSN 2470-1343
    ISSN (online) 2470-1343
    DOI 10.1021/acsomega.2c01036
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Antiviral Mechanisms of

    Laajala, Mira / Kalander, Kerttu / Consalvi, Sara / Amamuddy, Olivier Sheik / Bishop, Özlem Tastan / Biava, Mariangela / Poce, Giovanna / Marjomäki, Varpu

    Pharmaceutics

    2023  Volume 15, Issue 3

    Abstract: Enteroviruses are one of the most abundant groups of viruses infecting humans, and yet there are no approved antivirals against them. To find effective antiviral compounds against enterovirus B group viruses, an in-house chemical library was screened. ... ...

    Abstract Enteroviruses are one of the most abundant groups of viruses infecting humans, and yet there are no approved antivirals against them. To find effective antiviral compounds against enterovirus B group viruses, an in-house chemical library was screened. The most effective compounds against Coxsackieviruses B3 (CVB3) and A9 (CVA9) were CL212 and CL213, two
    Language English
    Publishing date 2023-03-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2527217-2
    ISSN 1999-4923
    ISSN 1999-4923
    DOI 10.3390/pharmaceutics15031028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Slipknot or Crystallographic Error: A Computational Analysis of the

    Tata, Rolland B / Alsulami, Ali F / Sheik Amamuddy, Olivier / Blundell, Tom L / Tastan Bishop, Özlem

    International journal of molecular sciences

    2022  Volume 23, Issue 3

    Abstract: The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of ... ...

    Abstract The presence of protein structures with atypical folds in the Protein Data Bank (PDB) is rare and may result from naturally occurring knots or crystallographic errors. Proper characterisation of such folds is imperative to understanding the basis of naturally existing knots and correcting crystallographic errors. If left uncorrected, such errors can frustrate downstream experiments that depend on the structures containing them. An atypical fold has been identified in
    MeSH term(s) Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; Molecular Dynamics Simulation ; Plasmodium falciparum/enzymology ; Plasmodium falciparum/genetics ; Protein Conformation ; Protein Domains ; Protein Folding ; Protozoan Proteins/chemistry ; Protozoan Proteins/genetics ; Sequence Alignment/methods ; Sequence Analysis, Protein ; Sequence Homology, Amino Acid ; Tetrahydrofolate Dehydrogenase/chemistry ; Tetrahydrofolate Dehydrogenase/genetics
    Chemical Substances Protozoan Proteins ; Tetrahydrofolate Dehydrogenase (EC 1.5.1.3)
    Language English
    Publishing date 2022-01-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms23031514
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  4. Article: MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics.

    Sheik Amamuddy, Olivier / Glenister, Michael / Tshabalala, Thulani / Tastan Bishop, Özlem

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 5059–5071

    Abstract: The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network ...

    Abstract The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. Altogether, these tools allow for the exploration of protein dynamics at various levels of detail, spanning single residue perturbations and weighted contact network representations, to global residue centrality measurements and the investigation of global protein motion. Typically, following molecular dynamic simulations designed to investigate intrinsic and extrinsic protein perturbations (for instance induced by allosteric and orthosteric ligands, protein binding, temperature, pH and mutations), this selection of tools can be used to further describe protein dynamics. This may lead to the discovery of key residues involved in biological processes, such as drug resistance. The server simplifies the set-up required for running these tools and visualizing their results. Several scripts from the tool suites were updated and new ones were also added and integrated with 2D/3D visualization via the web interface. An embedded work-flow, integrated documentation and visualization tools shorten the number of steps to follow, starting from calculations to result visualization. The Django-powered web server (available at https://mdmtaskweb.rubi.ru.ac.za/) is compatible with all major web browsers. All scripts implemented in the web platform are freely available at https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web and https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.
    Language English
    Publishing date 2021-09-02
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.08.043
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  5. Article: Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 M

    Sheik Amamuddy, Olivier / Afriyie Boateng, Rita / Barozi, Victor / Wavinya Nyamai, Dorothy / Tastan Bishop, Özlem

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 6431–6455

    Abstract: The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of mutations is a relatively unexplored field. Here, we established ... ...

    Abstract The rational search for allosteric modulators and the allosteric mechanisms of these modulators in the presence of mutations is a relatively unexplored field. Here, we established novel
    Language English
    Publishing date 2021-11-25
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.11.016
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  6. Article: Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance.

    Okeke, Chiamaka Jessica / Musyoka, Thommas Mutemi / Sheik Amamuddy, Olivier / Barozi, Victor / Tastan Bishop, Özlem

    Computational and structural biotechnology journal

    2021  Volume 19, Page(s) 5647–5666

    Abstract: Continually emerging resistant strains of malarial parasites to current drugs present challenges. Understanding the underlying resistance mechanisms, especially those linked to allostery is, thus, highly crucial for drug design. This forms the main ... ...

    Abstract Continually emerging resistant strains of malarial parasites to current drugs present challenges. Understanding the underlying resistance mechanisms, especially those linked to allostery is, thus, highly crucial for drug design. This forms the main concern of the paper through a case study of falcipain 2 (FP-2) and its mutations, some of which are linked to artemisinin (ART) drug resistance. Here, we applied a variety of
    Language English
    Publishing date 2021-10-08
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.10.011
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Impact of Early Pandemic Stage Mutations on Molecular Dynamics of SARS-CoV-2 M

    Sheik Amamuddy, Olivier / Verkhivker, Gennady M / Tastan Bishop, Özlem

    Journal of chemical information and modeling

    2020  Volume 60, Issue 10, Page(s) 5080–5102

    Abstract: A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease ( ... ...

    Abstract A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (M
    MeSH term(s) Betacoronavirus/chemistry ; Betacoronavirus/genetics ; Binding Sites ; COVID-19 ; Coronavirus 3C Proteases ; Coronavirus Infections/epidemiology ; Coronavirus Infections/virology ; Cysteine Endopeptidases/chemistry ; Cysteine Endopeptidases/genetics ; Humans ; Molecular Dynamics Simulation ; Mutation ; Pandemics ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/virology ; Point Mutation ; Protein Conformation ; Protein Multimerization ; SARS-CoV-2 ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/genetics
    Chemical Substances Viral Nonstructural Proteins ; Cysteine Endopeptidases (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
    Keywords covid19
    Language English
    Publishing date 2020-09-16
    Publishing country United States
    Document type Journal Article
    ZDB-ID 190019-5
    ISSN 1549-960X ; 0095-2338
    ISSN (online) 1549-960X
    ISSN 0095-2338
    DOI 10.1021/acs.jcim.0c00634
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    In stock of ZB MED Cologne/Königswinter

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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
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  8. Article: MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics

    Sheik Amamuddy, Olivier / Glenister, Michael / Tshabalala, Thulani / Tastan Bishop, Özlem

    Computational and Structural Biotechnology Journal. 2021, v. 19

    2021  

    Abstract: The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network ...

    Abstract The web server, MDM-TASK-web, combines the MD-TASK and MODE-TASK software suites, which are aimed at the coarse-grained analysis of static and all-atom MD-simulated proteins, using a variety of non-conventional approaches, such as dynamic residue network analysis, perturbation-response scanning, dynamic cross-correlation, essential dynamics and normal mode analysis. Altogether, these tools allow for the exploration of protein dynamics at various levels of detail, spanning single residue perturbations and weighted contact network representations, to global residue centrality measurements and the investigation of global protein motion. Typically, following molecular dynamic simulations designed to investigate intrinsic and extrinsic protein perturbations (for instance induced by allosteric and orthosteric ligands, protein binding, temperature, pH and mutations), this selection of tools can be used to further describe protein dynamics. This may lead to the discovery of key residues involved in biological processes, such as drug resistance. The server simplifies the set-up required for running these tools and visualizing their results. Several scripts from the tool suites were updated and new ones were also added and integrated with 2D/3D visualization via the web interface. An embedded work-flow, integrated documentation and visualization tools shorten the number of steps to follow, starting from calculations to result visualization. The Django-powered web server (available at https://mdmtaskweb.rubi.ru.ac.za/) is compatible with all major web browsers. All scripts implemented in the web platform are freely available at https://github.com/RUBi-ZA/MD-TASK/tree/mdm-task-web and https://github.com/RUBi-ZA/MODE-TASK/tree/mdm-task-web.
    Keywords Internet ; biotechnology ; computer software ; drug resistance ; ligands ; pH ; temperature ; user interface
    Language English
    Size p. 5059-5071.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2021.08.043
    Database NAL-Catalogue (AGRICOLA)

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  9. Article: Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of

    Sheik Amamuddy, Olivier / Musyoka, Thommas Mutemi / Boateng, Rita Afriyie / Zabo, Sophakama / Tastan Bishop, Özlem

    Computational and structural biotechnology journal

    2020  Volume 18, Page(s) 1103–1120

    Abstract: Pyrazinamide (PZA) is the only first-line antitubercular drug active against ... ...

    Abstract Pyrazinamide (PZA) is the only first-line antitubercular drug active against latent
    Language English
    Publishing date 2020-05-18
    Publishing country Netherlands
    Document type Journal Article
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2020.05.009
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Impact of early pandemic stage mutations on molecular dynamics of SARS-CoV-2 Mpro:

    Sheik Amamuddy, Olivier / Verkhivker, Gennady M / Bishop, Ozlem Tastan

    2020  

    Abstract: A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its ... ...

    Abstract A new coronavirus (SARS-CoV-2) is a global threat to world health and economy. Its dimeric main protease (Mpro), which is required for the proteolytic cleavage of viral precursor proteins, is a good candidate for drug development owing to its conservation and the absence of a human homolog. Improving our understanding of Mpro behavior can accelerate the discovery of effective therapies to reduce mortality. All-atom molecular dynamics (MD) simulations (100 ns) of 50 mutant Mpro dimers obtained from filtered sequences from the GISAID database were analyzed using root-mean-square deviation, root-mean-square fluctuation, Rg, averaged betweenness centrality, and geometry calculations.
    Keywords covid19
    Language English
    Publishing country za
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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