moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari)
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Scroll down 👇![mavzu:moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari reja: muammo ta'rifi ...................................................................................................... 3 docking yondashuvlari .......................................................................................... 4 shaklni to'ldirish ................................................................................................. 4 simulyatsiya ....................................................................................................... 5 docking mexanikasi .............................................................................................. 6 qidiruv algoritmi [ tahrir ] ................................................................................. 6 baholash funktsiyasi .......................................................................................... 8 docking baholash [ tahrirlash ] ............................................................................. 9 docking aniqligi ............................................................................................... 10 boyitish omili ................................................................................................... 10 istiqbolli ........................................................................................................... 10 benchmarking .................................................................................................. 10 molekulyar docking tarkibiy molekulyar biologiya va kompyuter yordamida dori-darmonlarni loyihalashda asosiy vositadir. ligand-oqsilni biriktirishning maqsadi ma'lum uch o'lchovli tuzilishga ega bo'lgan ligandning asosiy bog'lanish rejimini (moddalarini) bashorat qilishdir. muvaffaqiyatli o'rnatish usullari yuqori o'lchamli bo'shliqlarni samarali qidiradi va nomzodlarni o'rnatishni to'g'ri tartiblovchi reyting funksiyasidan foydalanadi. docking birikmalarning katta kutubxonalarida virtual skrini](/media/previews/pages/p1_261014.webp "moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari) - Page 1")
![ngni amalga oshirish, natijalarni tartiblash va ligandlarning maqsadni qanday inhibe qilishiga oid tizimli farazlarni taklif qilish uchun ishlatilishi mumkin, bu qo'rg'oshinni optimallashtirishda bebahodir. docking uchun kirish tuzilmalarini o'rnatish xuddi o'rnatishning o'zi kabi muhim va stokastik qidiruv usullarining natijalarini tahlil qilish ba'zan noaniq bo'lishi mumkin. ushbu bobda molekulyar docking dasturiy ta'minotining foni va nazariyasi muhokama qilinadi va eng ko'p keltirilgan dock dasturiy ta'minotidan foydalanishni o'z ichiga oladi. molekulyar modellashtirish sohasida docking , barqaror kompleks hosil qilish uchun ligand va maqsad bir-biriga bog'langanda bir molekulaning ikkinchisiga afzal yo'nalishini taxmin qiladigan usuldir . [1] oʻz navbatida afzal koʻrilgan yoʻnalish haqidagi bilimlar , masalan, ball funksiyalari yordamida ikki molekula oʻrtasidagi bogʻlanish kuchini yoki bogʻlanish yaqinligini bashorat qilish uchun ishlatilishi mumkin . https://en.wikipedia.org/wiki/molecular_modeling https://en.wikipedia.org/wiki/supramolecular_chemistry https://en.wikipedia.org/wiki/supramolecular_chemistry https://en.wikipedia.org/wiki/ligand_(biochemistry) https://en.wikipedia.org/wiki/binding_(molecular) https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid8804827-1 https://en.wikipedia.org/wiki/scoring_functions_for_docking https://en.wikipedia.org/wiki/dissociation_constant#protein-ligand_binding barqaror kompleks hosil qiluvchi kichik molekulali ligandni (yashil) oqsil nishoniga (qora) ulashning sxematik tasviri.davomiyligi: 13 soniya.0:13kichkina molekulaning (yashil) beta-2 adrenergik g-oqsil bilan bog'langan retseptorining kristal …](/media/previews/pages/p2_261014.webp "moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari) - Page 2")
![gnal turiga ta'sir qilishi mumkin (masalan, agonizma va antagonizm ). shuning uchun docking ishlab chiqarilgan signalning kuchini va turini bashorat qilish uchun foydalidir. molekulyar o'rnatish - bu kichik molekula ligandlarining tegishli maqsadli bog'lanish joyiga bog'lanish-konformatsiyasini bashorat qilish qobiliyati tufayli tuzilishga asoslangan dori dizaynida eng ko'p qo'llaniladigan usullardan biridir . bog'lanish harakatining tavsifi dori vositalarini oqilona loyihalashda , shuningdek, asosiy biokimyoviy jarayonlarni yoritishda muhim rol o'ynaydi. [2] [3] muammo ta'rifi molekulyar o'rnatishni "qulflash va kalit" muammosi deb hisoblash mumkin , bunda "qulf " ni ochadigan "kalit" ning to'g'ri nisbiy yo'nalishini topishni xohlaydi (qulf yuzasida joylashgan joy ). kalit teshigi, kalit kiritilgandan keyin uni qaysi tomonga burish kerakligi va hokazo). bu erda oqsilni "qulf", ligandni esa "kalit" deb hisoblash mumkin. molekulyar ulanishni optimallashtirish muammosi sifatida https://en.wikipedia.org/wiki/beta-2_adrenergic_receptor https://en.wikipedia.org/wiki/beta-2_adrenergic_receptor https://en.wikipedia.org/wiki/g_protein%e2%80%93coupled_receptor https://en.wikipedia.org/wiki/crystal_structure https://en.wikipedia.org/wiki/protein_data_bank https://www.rcsb.org/structure/3sn6 https://en.wikipedia.org/wiki/proteins https://en.wikipedia.org/wiki/peptide https://en.wikipedia.org/wiki/nucleic_acids https://en.wikipedia.org/wiki/nucleic_acids https://en.wikipedia.org/wiki/carbohydrates https://en.wikipedia.org/wiki/lipids https://en.wikipedia.org/wiki/signal_transduction https://en.wikipedia.org/wiki/signal_transduction https://en.wikipedia.org/wiki/agonist https://en.wikipedia.org/wiki/antagonist_(pharmacology) https://en.wikipedia.org/wiki/small_molecule https://en.wikipedia.org/wiki/binding_site https://en.wikipedia.org/wiki/drug_design https://en.wikipedia.org/wiki/rational_drug_design https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid15520816-2 ht](/media/previews/pages/p3_261014.webp "moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari) - Page 3")
![tps://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid15520816-2 https://en.wikipedia.org/wiki/file:docking_representation_2.png ta'riflash mumkin, bu ma'lum bir qiziqish oqsiliga bog'langan ligandning "eng mos" yo'nalishini tavsiflaydi. biroq, ligand ham, oqsil ham moslashuvchan bo'lganligi sababli, "qulf va kalit" dan ko'ra " qo'l-qo'lqop" analogiyasi ko'proq mos keladi . [4] o'rnatish jarayonida ligand va oqsil umumiy "eng mos" ga erishish uchun o'z konformatsiyasini moslashtiradi va umumiy bog'lanishga olib keladigan bunday konformatsion moslashuv "induced-fit" deb ataladi . [5] molekulyar docking tadqiqotlari molekulyar tanib olish jarayonini hisoblash simulyatsiyasiga qaratilgan . u oqsil va ligand uchun optimallashtirilgan konformatsiyaga va oqsil va ligand o'rtasidagi nisbiy yo'nalishga erishishga qaratilgan, shunda umumiy tizimning erkin energiyasi minimallashtiriladi. docking yondashuvlari ikkita yondashuv molekulyar docking hamjamiyatida ayniqsa mashhur. yondashuvlardan biri oqsil va ligandni bir-birini to'ldiruvchi sirt sifatida tasvirlaydigan mos keladigan texnikadan foydalanadi. [6] [7] [8] ikkinchi yondashuv ligand-oqsil juftlik o'zaro ta'sir energiyalari hisoblangan haqiqiy o'rnatish jarayonini simulyatsiya qiladi. [9] har ikkala yondashuv ham muhim afzalliklarga, shuningdek, ba'zi cheklovlarga ega. bular quyida …](/media/previews/pages/p4_261014.webp "moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari) - Page 4")
![hqa yondashuv - asosiy zanjir atomlaridagi burilishlar yordamida oqsilning hidrofobik xususiyatlarini tasvirlash. https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid1719636-4 https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid15046985-5 https://en.wikipedia.org/wiki/molecular_recognition https://en.wikipedia.org/wiki/gibbs_free_energy https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-wipke_2000-6 https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-wipke_2000-6 https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-morris_1998-8 https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-pmid14648625-9 https://en.wikipedia.org/wiki/docking_(molecular)#cite_note-shoichet_2004-10 https://en.wikipedia.org/wiki/van_der_waals_surface https://en.wikipedia.org/w/index.php?title=complementary_surface&action=edit&redlink=1 https://en.wikipedia.org/wiki/solvent-accessible_surface_area https://en.wikipedia.org/wiki/solvent-accessible_surface_area yana bir yondashuv furye shakli tavsiflovchi texnikasidan foydalanishdir. [11] [12] [13] shaklni toʻldirishga asoslangan yondashuvlar odatda tez va mustahkam boʻlsa-da, ular odatda ligand/oqsil konformatsiyasidagi harakatlar yoki dinamik oʻzgarishlarni aniq modellashtira olmaydi, garchi soʻnggi oʻzgarishlar bu usullar ligandlarning moslashuvchanligini tekshirishga imkon beradi. shaklni to'ldirish usullari bir necha soniya ichida bir necha ming ligandlarni tezda skanerlashi va aslida ular oqsilning faol joyida bog'lanishi mumkinligini aniqlay oladi va odatda hatto oqsil-oqsil o'zaro ta'sirida ham kengaytirilishi mumkin. ular, shuningdek, farmakoforga asoslangan yondashuvlarga ko'proq mos keladi , chunki ular optimal bog'lanishni topish uchun ligandlarning geometrik tavsiflaridan foydalanadilar. simulyatsiya docking jarayonini simulyatsiya qilish ancha murakkab. bunday yondashuvda oqsil va ligand ma'lum bir jismoniy masofa bilan ajralib turadi va ligand o'zining konformatsion bo'shlig'ida](/media/previews/pages/p5_261014.webp "moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari) - Page 5")
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mavzu:moddalarning biologik faolliklarini o’rganish (qsar/qspr va molekular docking dasturlari reja: muammo ta'rifi ...................................................................................................... 3 docking yondashuvlari .......................................................................................... 4 shaklni to'ldirish ................................................................................................. 4 simulyatsiya ....................................................................................................... 5 docking mexanikasi .............................................................................................. 6 qidiruv algoritmi [ tahrir ] ....................................................................................
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