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    Wyświetlanie 1-3 z 3
    Tytuł:
    Possible computational filter to detect proteins associated to influenza A subtype H1N1
    Autorzy:
    Polanco, Carlos
    Buhse, Thomas
    Castañón-González, Jorge
    Samaniego, José
    Powiązania:
    https://bibliotekanauki.pl/articles/1039197.pdf
    Data publikacji:
    2014
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    Polarity Index Method
    influenza A virus subtype H1N1
    drug design
    QSAR method
    Opis:
    The design of drugs with bioinformatics methods to identify proteins and peptides with a specific toxic action is increasingly recurrent. Here, we identify toxic proteins towards the influenza A virus subtype H1N1 located at the UniProt database. Our quantitative structure-activity relationship (QSAR) approach is based on the analysis of the linear peptide sequence with the so-called Polarity Index Method that shows an efficiency of 90% for proteins from the Uniprot Database. This method was exhaustively verified with the APD2, CPPsite, Uniprot, and AmyPDB databases as well as with the set of antibacterial peptides studied by del Rio et al. and Oldfield et al.
    Źródło:
    Acta Biochimica Polonica; 2014, 61, 4; 693-698
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Identification of proteins associated with Mycobacterium tuberculosis virulence pathway by their polar profile
    Autorzy:
    Polanco, Carlos
    Castañón-González, Jorge
    Mancilla, Raul
    Buhse, Thomas
    Samaniego, José
    Gimbel, Arturo
    Powiązania:
    https://bibliotekanauki.pl/articles/1039087.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    Mycobacterium tuberculosis bacteria virulence pathway
    Polarity Index Method
    Opis:
    With almost one third of the world population infected, tuberculosis is one of the most devastating diseases worldwide and it is a major threat to any healthcare system. With the mathematical-computational method named "Polarity Index Method", already published by this group, we identified, with high accuracy (70%), proteins related to Mycobacterium tuberculosis bacteria virulence pathway from the Tuberculist Database. The test considered the totality of proteins cataloged in the main domains: fungi, bacteria, and viruses from three databases: Antimicrobial Peptide Database (APD2), Tuberculist Database, Uniprot Database, and four antigens of Mycobacterium tuberculosis: PstS-1, 38-kDa, 19-kDa, and H37Rv ORF. The method described was calibrated with each database to achieve the same performance, showing a high percentage of coincidence in the identification of proteins associated with Mycobacterium tuberculosis bacteria virulence pathway located in the Tuberculist Database, and identifying a polar pattern regardless of the group studied. This method has already been used in the identification of diverse groups of proteins and peptides, showing that it is an effective discriminant. Its metric considers only one physico-chemical property, i.e. polarity.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 2; 191-196
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Identification of proteins associated with amyloidosis by polarity index method
    Autorzy:
    Polanco, Carlos
    Samaniego, José
    Uversky, Vladimir
    Castañón-González, Jorge
    Buhse, Thomas
    Leopold-Sordo, Marili
    Madero-Arteaga, Alejandro
    Morales-Reyes, Alicia
    Tavera-Sierra, Lourdes
    González-Bernal, Jesus
    Arias-Estrada, Miguel
    Powiązania:
    https://bibliotekanauki.pl/articles/1039130.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    Polarity index method
    natively unfolded proteins
    intrinsically disordered proteins
    natively folded proteins
    neurons
    amyloidosis
    amyloid
    amyloidogenic protein
    Opis:
    There is a natural protein form, insoluble and resistant to proteolysis, adopted by many proteins independently of their amino acid sequences via specific misfolding-aggregation process. This dynamic process occurs in parallel with or as an alternative to physiologic folding, generating toxic protein aggregates that are deposited and accumulated in various organs and tissues. These proteinaceous deposits typically represent bundles of β-sheet-enriched fibrillar species known as the amyloid fibrils that are responsible for serious pathological conditions, including but not limited to neurodegenerative diseases, grouped under the term amyloidoses. The proteins that might adopt this fibrillar conformation are some globular proteins and natively unfolded (or intrinsically disordered) proteins. Our work shows that intrinsically disordered and intrinsically ordered proteins can be reliably identified, discriminated, and differentiated by analyzing their polarity profiles generated using a computational tool known as the polarity index method (Polanco & Samaniego, 2009; Polanco et al., 2012; 2013; 2013a; 2014; 2014a; 2014b; 2014c; 2014d). We also show that proteins expressed in neurons can be differentiated from proteins in these two groups based on their polarity profiles, and also that this computational tool can be used to identify proteins associated with amyloidoses. The efficiency of the proposed method is high (i.e. 70%) as evidenced by the analysis of peptides and proteins in the APD2 database (2012), AVPpred database (2013), and CPPsite database (2013), the set of selective antibacterial peptides from del Rio et al. (2001), the sets of natively unfolded and natively folded proteins from Oldfield et al. (2005), the set of human revised proteins expressed in neurons, and non-human revised proteins expressed in neurons, from the Uniprot database (2014), and also the set of amyloidogenic proteins from the AmyPDB database (2014).
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 1; 41-55
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
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