Yuav ua li cas yog tias peb tuaj yeem siv kev txawj ntse los teb ib qho ntawm lub neej tsis meej tshaj plaws - protein folding? Cov kws tshawb fawb tau ua haujlwm rau qhov no tau ntau xyoo lawm.
Cov tshuab tam sim no tuaj yeem kwv yees cov qauv protein nrog qhov ua tau zoo tshaj plaws uas siv cov qauv kev kawm sib sib zog nqus, hloov kho kev txhim kho tshuaj, biotechnology, thiab peb paub txog cov txheej txheem lom neeg.
Koom nrog kuv ntawm kev tshawb fawb mus rau hauv qhov txaus nyiam ntawm AI protein folding, qhov twg cov cuab yeej siv niaj hnub sib tsoo nrog qhov nyuaj ntawm lub neej nws tus kheej.
Unraveling Mystery ntawm Protein Folding
Proteins ua haujlwm hauv peb lub cev zoo li lub tshuab me me los ua cov haujlwm tseem ceeb xws li rhuav tshem cov zaub mov lossis thauj cov pa oxygen. Lawv yuav tsum tau muab tais kom raug rau lawv kom ua haujlwm zoo, ib yam li tus yuam sij yuav tsum raug txiav kom raug kom haum rau hauv lub xauv. Thaum cov protein tsim, cov txheej txheem folding nyuaj heev pib.
Protein folding yog cov txheej txheem uas ntev chains ntawm cov amino acids, cov protein lub tsev blocks, quav rau hauv peb-dimensional qauv uas dictate cov hauj lwm ntawm cov protein.
Xav txog ib txoj hlua ntev ntawm cov hlaws dai uas yuav tsum tau txiav txim rau hauv daim ntawv meej; Qhov no yog qhov tshwm sim thaum cov protein folds. Txawm li cas los xij, tsis zoo li cov hlaws dai, cov amino acids muaj cov yam ntxwv tshwj xeeb thiab cuam tshuam nrog lwm tus hauv ntau txoj hauv kev, ua rau cov protein folding txoj kev nyuaj thiab rhiab heev.
Daim duab ntawm no sawv cev rau tib neeg hemoglobin, uas yog lub npe hu ua folded protein
Proteins yuav tsum ceev ceev thiab meej, los yog lawv yuav ua misfolded thiab puas. Qhov ntawd tuaj yeem ua rau muaj mob xws li Alzheimer's thiab Parkinson's. Kub, siab, thiab muaj lwm yam molecules nyob rau hauv lub cell tag nrho cov muaj feem xyuam rau cov txheej txheem folding.
Tom qab ntau xyoo ntawm kev tshawb fawb, cov kws tshawb fawb tseem tab tom sim ua kom paub tseeb tias cov protein ntau npaum li cas.
Ua tsaug, kev nce qib hauv kev txawj ntse txawj ntse yog txhim kho kev txhim kho hauv kev lag luam. Cov kws tshawb fawb tuaj yeem cia siab tias cov qauv ntawm cov protein ntau yog qhov tseeb dua li yav dhau los los ntawm kev siv tshuab kawm algorithms los tshuaj xyuas cov ntaub ntawv loj heev.
Qhov no muaj peev xwm hloov kho kev tsim kho thiab ua kom peb cov kev paub txog molecular ntawm tus mob.
Cov tshuab puas tuaj yeem ua tau zoo dua?
Pa Protein Folding Techniques muaj kev txwv
Cov kws tshawb fawb tau sim txheeb xyuas cov protein folding rau ntau xyoo lawm, tab sis cov txheej txheem intricacy tau ua rau qhov no nyuaj.
Cov qauv txheej txheem kev kwv yees cov qauv siv cov qauv siv sib xyaw ua ke ntawm cov qauv kev sim thiab kev ua qauv hauv computer, txawm li cas los xij, cov qauv no txhua tus muaj qhov tsis zoo.
Kev sim cov txheej txheem xws li X-ray crystallography thiab nuclear magnetic resonance (NMR) tuaj yeem siv sijhawm ntev thiab kim. Thiab, cov qauv hauv computer qee zaum tso siab rau cov kev xav tau yooj yim, uas tuaj yeem ua rau muaj kev kwv yees yuam kev.
AI tuaj yeem kov yeej cov teeb meem no
Luckily, artificial txawj ntse yog muab cov lus cog tseg tshiab rau qhov tseeb thiab muaj txiaj ntsig cov qauv kev twv ua ntej. Kev kawm tshuab algorithms tuaj yeem tshawb xyuas cov ntaub ntawv loj heev. Thiab, lawv nthuav tawm cov qauv uas tib neeg yuav nco.
Qhov no tau ua rau kev tsim cov cuab yeej software tshiab thiab cov platforms muaj peev xwm kwv yees cov qauv protein nrog qhov tsis sib xws.
Qhov Zoo Tshaj Plaws Tshuab Kawm Algorithms rau Protein Structure Prediction
AlphaFold system tsim los ntawm Google's DeepMind pab neeg no yog ib qho kev vam meej tshaj plaws hauv cheeb tsam no. Nws tau txais kev vam meej hauv xyoo tas los no los ntawm kev siv tob kawm kev kawm los kwv yees cov qauv ntawm cov proteins raws li lawv cov amino acid sequences.
Neural tes hauj lwm, txhawb vector machines, thiab random hav zoov yog ib qho ntawm ntau txoj kev kawm tshuab uas qhia tau hais tias cog lus rau kwv yees cov qauv protein.
Cov algorithms no tuaj yeem kawm los ntawm cov ntaub ntawv loj heev. Thiab, lawv tuaj yeem cia siab tias muaj kev sib raug zoo ntawm cov amino acids sib txawv. Yog li, cia saib seb nws ua haujlwm li cas.
Co-evolutionary Analyzes thiab Thawj AlphaFold Generation
Cov kev vam meej ntawm AlphaFold yog tsim los ntawm tus qauv sib sib zog nqus neural network uas tau tsim los siv kev tshuaj xyuas kev sib koom ua ke. Lub tswv yim ntawm kev sib koom ua ke hais tias yog tias ob lub amino acids hauv cov protein cuam tshuam nrog ib leeg, lawv yuav txhim kho ua ke kom lawv txoj haujlwm txuas.
Cov kws tshawb fawb tuaj yeem tshawb pom cov khub ntawm cov amino acids uas yuav muaj nyob rau hauv cov qauv 3D los ntawm kev sib piv cov amino acid sequences ntawm ntau cov proteins uas zoo sib xws.
Cov ntaub ntawv no yog lub hauv paus rau thawj iteration ntawm AlphaFold. Nws kwv yees qhov ntev ntawm cov amino acid khub nrog rau cov ces kaum ntawm peptide bonds uas txuas lawv. Txoj kev no tau ua tiav tag nrho cov txheej txheem ua ntej rau kev kwv yees cov qauv protein los ntawm cov kab ke, txawm hais tias qhov tseeb tseem raug txwv rau cov proteins uas tsis muaj cov qauv tsim.
AlphaFold 2: Ib Txoj Kev Tshiab Radically
AlphaFold2 yog lub khoos phis tawj software tsim los ntawm DeepMind uas siv cov protein cov amino acid sib lawv liag los kwv yees 3D qauv ntawm cov protein.
Qhov no yog qhov tseem ceeb vim hais tias cov qauv ntawm cov protein hais tias nws ua haujlwm li cas, thiab kev nkag siab txog nws txoj haujlwm tuaj yeem pab cov kws tshawb fawb tsim cov tshuaj uas tsom rau cov protein.
Lub AlphaFold2 neural network tau txais kev nkag mus rau cov protein cov amino acid ib ntus thiab cov ntsiab lus hais txog yuav ua li cas cov kab ke sib piv rau lwm cov kab ke hauv cov ntaub ntawv (qhov no yog hu ua "ib ntu sib dhos").
Lub neural network ua rau kev twv ua ntej txog cov protein cov qauv 3D raws li cov tswv yim no.
Dab tsi Teem nws Sib nrug ntawm AlphaFold2?
Hauv kev sib piv rau lwm txoj hauv kev, AlphaFold2 kwv yees qhov tiag 3D qauv ntawm cov protein ntau dua li tsuas yog kev sib cais ntawm cov khub ntawm cov amino acids lossis cov ces kaum ntawm cov ntawv cog lus txuas rau lawv (raws li algorithms ua ntej tau ua).
Txhawm rau kom cov neural network xav txog cov qauv tag nrho ib zaug, cov qauv yog encoded kawg-rau-kawg.
Lwm tus yam ntxwv tseem ceeb ntawm AlphaFold2 yog tias nws muaj kev kwv yees tias nws ntseeg siab npaum li cas hauv nws qhov kev kwv yees. Qhov no yog nthuav tawm raws li cov xim coding ntawm cov qauv xav tau, nrog liab sawv cev rau kev ntseeg siab thiab xiav qhia tias tsis muaj kev ntseeg siab.
Qhov no yog qhov tseem ceeb vim nws qhia cov kws tshawb fawb txog kev ruaj ntseg ntawm qhov kev twv ua ntej.
Kev kwv yees qhov sib xyaw ua ke ntawm ob peb ntu
Qhov tseeb nthuav dav ntawm Alphafold2, lub npe hu ua Alphafold Multimer, kwv yees cov qauv sib xyaw ua ke ntawm ntau ntu. Nws tseem muaj qhov yuam kev siab txawm tias nws ua tau zoo dua li cov txheej txheem ua ntej. Tsuas yog 25% ntawm 4500 protein complexes tau ua tiav kev kwv yees.
70% ntawm cov cheeb tsam ntxhib ntawm kev sib cuag tau raug kwv yees kom raug, tab sis kev txheeb ze ntawm ob lub proteins tsis raug. Thaum qhov nruab nrab qhov sib npaug ntawm qhov tob yog tsawg dua li ntawm 30 ntu, qhov tseeb ntawm Alphafold multimer kev kwv yees poob qis heev.
Yuav Siv Alphafold Predictions li cas
Cov qauv kwv yees los ntawm AlphaFold muaj nyob rau hauv tib cov ntaub ntawv tawm tswv yim thiab tuaj yeem siv tib yam li cov qauv kev sim. Nws yog ib qho tseem ceeb uas yuav tau coj mus rau hauv tus account qhov tseeb kwv yees muaj nrog tus qauv txhawm rau tiv thaiv kev nkag siab yuam kev.
Nws yog qhov tshwj xeeb tshaj yog pab tau rau cov txheej txheem nyuaj xws li interwoven homomers lossis cov proteins uas tsuas yog quav hauv qhov muaj
tsis paub ligand.
Qee Qhov Kev Sib Tw
Qhov teeb meem tseem ceeb hauv kev siv cov qauv kev kwv yees yog kev nkag siab txog kev hloov pauv, ligand selectivity, tswj, allostery, tom qab kev hloov pauv, thiab kinetics ntawm kev khi yam tsis tau nkag mus rau cov ntaub ntawv protein thiab biophysical.
Tshuab kawm thiab physics-based molecular dynamics kev tshawb fawb tuaj yeem siv los daws qhov teeb meem no.
Cov kev tshawb nrhiav no tuaj yeem tau txais txiaj ntsig los ntawm kev tshwj xeeb thiab siv computer architecture. Thaum AlphaFold tau ua tiav qhov kev nce qib loj heev hauv kev kwv yees cov qauv ntawm cov protein, tseem muaj ntau yam uas yuav tsum tau kawm hauv thaj chaw ntawm cov qauv biology, thiab AlphaFold kev kwv yees tsuas yog qhov pib rau kev kawm yav tom ntej.
Dab tsi yog Lwm Cov Cuab Yeej Zoo Tshaj Plaws?
RoseTTAFold
RoseTTAFold, tsim los ntawm University of Washington cov kws tshawb fawb, ib yam li siv cov kev kawm sib sib zog nqus los kwv yees cov qauv ntawm cov protein, tab sis nws kuj tseem koom nrog txoj hauv kev tshiab hu ua "torsion angle dynamics simulations" los txhim kho cov qauv kev kwv yees.
Txoj kev no tau txhawb nqa cov txiaj ntsig thiab tej zaum yuav muaj txiaj ntsig hauv kev kov yeej cov kev txwv ntawm cov cuab yeej AI protein folding uas twb muaj lawm.
trRosetta ua
Lwm lub cuab yeej, trRosetta, kwv yees protein folding los ntawm kev siv a neural network tau kawm txog tsheej lab ntawm cov protein ntau thiab cov qauv.
Nws kuj tseem siv cov txheej txheem "template-based modeling" los tsim cov kev kwv yees kom meej dua los ntawm kev sib piv cov hom phiaj protein kom sib piv cov qauv paub.
Nws tau raug pom tias trRosetta muaj peev xwm kwv yees cov qauv ntawm cov protein me me thiab cov protein ntau.
DeepMetaPSICOV
DeepMetaPSICOV yog lwm lub cuab yeej uas tsom rau kev kwv yees cov duab sib cuag nrog cov protein. Cov no, yog siv los ua ib qho kev qhia rau kwv yees protein folding. Nws siv kawm tob txoj hauv kev los kwv yees qhov muaj feem cuam tshuam ntawm cov khoom seem hauv cov protein.
Cov no yog tom qab siv los kwv yees tag nrho daim ntawv qhia kev sib cuag. DeepMetaPSICOV tau pom muaj peev xwm hauv kev kwv yees cov qauv protein nrog qhov raug zoo, txawm tias yav dhau los txoj hauv kev ua tsis tiav.
Lub Neej Tom Ntej Yuav Zoo Li Cas?
Lub neej yav tom ntej ntawm AI protein folding yog ci. Kev kawm sib sib zog nqus-raws li algorithms, tshwj xeeb tshaj yog AlphaFold2, tsis ntev los no tau ua tiav zoo hauv kev ntseeg siab kwv yees cov qauv protein.
Qhov kev tshawb pom no muaj peev xwm los hloov cov tshuaj txhim kho los ntawm kev tso cai rau cov kws tshawb fawb kom nkag siab zoo txog cov qauv thiab kev ua haujlwm ntawm cov protein, uas yog cov hom phiaj kho mob.
Txawm li cas los xij, cov teeb meem xws li kev kwv yees cov protein complexes thiab kuaj pom qhov ua haujlwm tiag tiag ntawm cov qauv kev cia siab tseem nyob. Kev tshawb fawb ntxiv yog xav tau los daws cov teeb meem no thiab ua kom qhov tseeb thiab kev ntseeg siab ntawm AI protein folding algorithms.
Txawm li cas los xij, cov txiaj ntsig zoo ntawm cov thev naus laus zis no muaj ntau heev, thiab nws muaj peev xwm ua rau kev tsim cov tshuaj zoo dua thiab meej.
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