Yazar "Saracbasi, Osman" seçeneğine göre listele

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    Investigation of protein quaternary structure via stoichiometry and symmetry information
    (Public Library Science, 2018) Korkmaz, Selcuk; Duarte, Jose M.; Prlic, Andreas; Goksuluk, Dincer; Zararsiz, Gokmen; Saracbasi, Osman; Burley, Stephen K.
    The Protein Data Bank (PDB) is the single worldwide archive of experimentally-determined three-dimensional (3D) structures of proteins and nucleic acids. As of January 2017, the PDB housed more than 125,000 structures and was growing by more than 11,000 structures annually. Since the 3D structure of a protein is vital to understand the mechanisms of biological processes, diseases, and drug design, correct oligomeric assembly information is of critical importance. Unfortunately, the biologically relevant oligomeric form of a 3D structure is not directly obtainable by X-ray crystallography, whilst in solution methods (NMR or single particle EM) it is known from the experiment. Instead, this information may be provided by the PDB Depositor as metadata coming from additional experiments, be inferred by sequence-sequence comparisons with similar proteins of known oligomeric state, or predicted using software, such as PISA (Proteins, Interfaces, Structures and Assemblies) or EPPIC (Evolutionary Protein Protein Interface Classifier). Despite significant efforts by professional PDB Biocurators during data deposition, there remain a number of structures in the archive with incorrect quaternary structure descriptions (or annotations). Further investigation is, therefore, needed to evaluate the correctness of quaternary structure annotations. In this study, we aim to identify the most probable oligomeric states for proteins represented in the PDB. Our approach evaluated the performance of four independent prediction methods, including text mining of primary publications, inference from homologous protein structures, and two computational methods (PISA and EPPIC). Aggregating predictions to give consensus results outperformed all four of the independent prediction methods, yielding 83% correct, 9% wrong, and 8% inconclusive predictions, when tested with a well-curated benchmark dataset. We have developed a freely-available web-based tool to make this approach accessible to researchers and PDB Biocurators (http://quatstruct.rcsb.org/).
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    Preformulation of Immediate Release Candesartan Cilexetil Tablets Using Full Factorial Experimental Design
    (Colegio Farmaceuticos Provincia De Buenos Aires, 2016) Yuce, Meral; Guven, Olgun; Karahan, Sevilay; Saracbasi, Osman; Capan, Yilmaz
    This work aimed compatibility and stability studies, five factor and two level (25) full factorial experimental design of immediate release candesartan cilexetil 32 mg tablets. Candesartan cilexetil is a drug substance, which has low solubility and chemical instability properties. Polyethylene glycol (PEG) 4000 showed stability protective property on candesartan cilexetil in tablets. Structural degradation of candesartan cilexetil was prevented by chemical reactions of terminal hydroxyl groups of PEG 4000 with carboxyl, N-H, N=N and anhydride groups of candesartan cilexetil. Stability protective mechanism was realized by converting crystalline candesartan cilexetil to amorphous form inside the amorphous region of PEG 4000. Stability evaluation showed that candesartan cilexetil could be protected ideally by PEG 4000 concentration of 2.5-10 % (w/w) in tablets. Dissolved drug from tablet could be predicted with high capability from statistical model, resulted from experimental design. Thus, stability and dissolution properties of candesartan cilexetil could be controlled in developed tablets.