Riba:
- Ikon kimanta hasashen tsarin AlphaFold tare da ƙimar amincewar pLDDT da guje wa da'awar dangane da ƙananan yankuna masu aminci.
- Ikon fassara makin docking azaman matsayin dangi, ba cikakkiyar kusanci ba, da kuma tabbatar da 'yan takara tare da ma'aunin kusancin gwaji.
- Ikon tace shawarwarin kwayoyin halitta masu amfani ta hanyar hadawa, kwanciyar hankali, da lafiyar halittu da kuma danganta tsinkaya mai mahimmanci zuwa gwajin jika
Don fahimtar abin da furotin ke yi, wajibi ne a san siffarsa mai girma uku; saboda tsarin yana ƙayyade aiki - aljihun catalytic na enzyme, daurin dauri na mai karɓa koyaushe yana tasowa daga siffarsa mai girma uku. Shekaru da yawa, buɗe tsarin furotin ya ɗauki watanni na gwaje-gwaje (X-ray crystallography, cryo-EM). AlphaFold da nau'ikan AI masu kama da wannan sun canza wannan hoton: suna iya tsinkayar tsarin nau'in furotin mai girma uku daga jerin amino acid tare da daidaito mai tsayi a cikin mintuna. Wannan juyin juya hali ne don injiniyan halittu; Amma sanin iyakokin juyin shine sharadin amfani da shi cikin aminci.
A cikin wannan rukunin, zaku koyi yadda ake amfani da AI a cikin tsinkayar tsari, docking na ƙwayoyin cuta (ƙididdigar yadda kuma yadda ƙarfin ƙaramin ƙwayar ƙwayar cuta ke ɗaure ga furotin) da ƙirar ƙirar ƙwayoyin cuta; A kowane mataki za ku koyi inda hasashen ya ƙare kuma gwajin ya fara.
AlphaFold: iko da iyaka
AlphaFold (samfurin ilmantarwa mai zurfi wanda ke tsinkayar tsarin 3D daga jerin sunadaran gina jiki) yana samar da ƙimar amincewa (pLDDT - ƙima daga 0 zuwa 100 yana nuna yadda ƙarfin ƙirar ke da kowane amino acid) tare da kowane tsinkaya. Babban pLDDT (> 90) gabaɗaya abin dogaro ne; Ƙananan yankuna (<50) sau da yawa yankuna ne masu rikice-rikice masu sassauƙa na furotin waɗanda ba su da ƙayyadaddun tsari-ko wuraren da ƙirar ba ta da tabbas. Iyakar AlphaFold ya sani shine yana ba da tsari guda ɗaya (ba motsin sunadaran ba), baya ƙirar ligand (ƙananan ƙwayoyin da ke ɗaure ga furotin) ko tasirin ion ƙarfe, ba koyaushe yana kama da dabarar tasirin maye gurbi ba, kuma baya bada garantin ko hadaddun zai haifar.
Tsanaki: AlphaFold hasashe ne da aka annabta, ba ginin gwaji bane. Da'awar hanyar da ta dogara da yankuna na ƙananan pLDDT ko gano aljihun magani a cikin waɗannan yankuna yaudara ne. Dole ne a tabbatar da mahimman tsari ta hanyar gwaji (crystallography, cryo-EM).
Docking: tsinkaya docking
Babban tambaya a cikin injiniyoyin ƙwayoyi da enzyme shine: "Shin wannan kwayar halitta tana ɗaure ga wannan furotin, kuma yaya ƙarfi?" Docking yana ƙididdige wannan kuma yana ƙididdige shi tare da aikin ƙira - ƙimanin ƙirar lissafi wanda ke kimanta ƙarfin ɗaure. Amma makin docking dangi ne kuma ba sa annabta alaƙar ɗaurin gaske; Adadin tabbataccen ƙarya yana da yawa. Sabbin hanyoyin tushen AI suna sa docking ɗin sauri da sauri kuma mafi daidai, amma sakamakon har yanzu jerin bincike ne - an tabbatar da shi ta hanyar ma'aunin kusanci (kamar SPR, ITC).
Tukwici: Yi amfani da docking zuwa jerin dubunnan ƙwayoyin cuta kafin gwaji, ba don cikakkiyar shawarar "daure/ba-daure" ba. Haɗawa da gwada kwayoyin halitta mafi girma 50 sun fi dacewa fiye da gwada 50 a bazuwar; Amma kwarewa ta yanke shawara.
Tsarin kwayoyin halitta da samfura masu haɓakawa
Samfuran ƙira-AI wanda zai iya “tsara” sabbin jerin sunadaran gina jiki ko ƙananan ƙwayoyin cuta-na iya ba da shawarar ƙwayoyin ɗan takara tare da kaddarorin da ake so: ingantaccen enzyme mai ƙarfi, sabon sigar magani wanda ke ɗaure ga manufa. Wannan yana da ƙarfi, amma yana da ramummuka guda biyu: ƙirar na iya ba da shawarar da ba za a iya haɗa su ba (na yuwuwar samar da sinadarai) ko jerin abubuwan da ba su dace ba. Shi ya sa a ko da yaushe ake tace abubuwan da ake samarwa ta hanyar haɗawa, kwanciyar hankali, da tsaro.
uku mini lokuta
Case 1 - Tsarin ya jagoranci kimanta. Ƙungiyar injiniyan enzyme tana aiki ba tare da tsarin gwaji na enzyme da aka yi niyya ba. AlphaFold ya nuna wurin da aka annabta mai aiki - yankin da enzyme ke aiwatar da halayen sinadaran; Tawagar ta tsara maye gurbi guda 3 a wannan yankin. A cikin gwajin, ɗayan ya ƙara aiki da sau 2.3. Amma maye gurbi biyu ba su yi aiki ba - tsinkayar tsinkaya, gwaji ya yanke shawarar.
Case 2 - Ƙarƙashin aminci yankin tarko. Wani dalibi yana so ya haɗa magani zuwa "aljihu" a cikin tsarin AlphaFold. Da yake duba taswirar pLDDT, ya ga cewa yankin ba shi da lafiya, mai yuwuwa wurin rashin lafiya tare da maki 38. An ƙaura zuwa tashar jirgin ruwa zuwa yankin aminci; ɓata watanni akan manufa mara kyau an hana.
Case 3 - Unsynthesizable shawara. Samfurin haɓakawa ya ba da shawarar kwayoyin halitta 200 waɗanda ke ɗaure ga manufa tare da babban maki. Lokacin da masanin kimiyyar ya tace shi, ya gano cewa kashi 40 cikin 100 na shi ba za a iya haɗa shi a zahiri ba ko kuma ba zai iya tsayawa ba. Da zarar tafkin da ya rage ya zama gaskiya, an haɗa 12.
Samfura huɗu masu kwafi
1) sharhin fitarwa na AlphaFold:
Matsayinku: masanin ilimin halitta. Zan ba ku taƙaitaccen pLDDTscore na Hasashen AlphaFold. Bambance ko wane yanki ne abin dogaro (> 90) da kuma waɗanda ake tuhuma (<50). Kar a kafa kowane tsarin da'awar dangane da ƙananan yankunan amincewa. Rubuta a cikin bugun ku cewa wannan ba ginin gwaji ba ne da yadda ake tabbatar da shi.
2) Tsarin tsarin aiki:
Matsayinku: masanin kimiyyar lissafi. Kwatanta ƙaramin aikin docking ɗin ƙwayoyin cuta don [protein manufa]: shirye-shiryen furotin, ma'anar ɗaurin aljihu, shirye-shiryen ligand, ƙira, jeri. Yi bayanin cewa makin docking BA cikakkiyar alaƙa ba ce kuma ta wace hanya ta gwaji (SPR/ITC) za a tabbatar da ita.
3) Halatta ƙira na maye gurbi:
Ina son shawarwari don maye gurbi don ƙara kwanciyar hankali na enzyme. Ga kowane shawarwarin: matsayi na manufa, ma'ana (maganganun tsarin) da yiwuwar haɗari (asarar aiki). Nuna cewa waɗannan zato ne kuma kowanne dole ne a gwada shi ta hanyar gwaji. Ba da shawarwari guda 5 kuma a ba da fifiko.
4) Tace mai inganci:
Ka ba ni ma'auni don kimanta kwayoyin halitta da aka ba da shawara ta hanyar ƙira mai ƙira: haɓakawa, kwanciyar hankali na sinadarai, sa hannun guba (caveats), nauyin kwayoyin halitta, da solubility. Faɗa mani bakin kofa wanda zan "kamata cire" ga kowane ma'auni. Wannan pre-tace; Shawarar ƙarshe ta kasance na dakin gwaje-gwaje mai jika.
Rauni mai ƙarfi / Ƙarfi mai ƙarfi
Rawanin faɗakarwa:
Zana maganin da ke ɗaure da wannan furotin.
Babu tsaro, babu synthesizability, babu tabbaci; AI yana samar da fitowar da ba ta dace ba, wacce ba za a iya tantancewa ba.
Ƙarfi mai ƙarfi:
Matsayinku: masanin kimiyyar lissafi. Bayar da dabarar SCREENING (tushen docking) don ƙananan ɓangarorin ƙwayoyin cuta waɗanda ke da yuwuwar ɗaure ga furotin [manufa]. Kada ku samar da kwayoyin siminti; a maimakon haka, bayyana mataki-mataki wane ɗakin karatu, wanne aljihu, wanda ya zira kwallaye da kuma wace tacewa don amfani, da yadda za a inganta kowane ɗan takara tare da kusancin gwaji.
Bambanci: mayar da hankali kan dabarun, iyawar haƙiƙa, tabbataccen fa'ida da wayar da kan tsaro.
Tsarin aiki da ingantaccen aiki
mataki
AI gudunmawa
iyaka
tabbatarwa
Hasashen tsari
AlphaFold 3D samfurin
A tsaye, ba tare da ligand ba
Cryo-EM / crystallography
Kimanta amana
Rahoton da aka ƙayyade na pLDDT
Ƙananan yanki ba a sani ba
Independent model kwatanta
docking
sauri iri
Maki ≠ kusanci
Ma'aunin SPR/ITC
tsarin maye gurbi
Shawarar ɗan takara
Ƙimar tasiri
gwajin aiki
samar da kwayoyin halitta
sabon dan takara
Synthesis / kwanciyar hankali
Chemist + gwajin jika
Matsalolin kwayoyin halitta: tsarin kunnawa
AlphaFold yana ba ku hoto guda ɗaya, daskararre; Duk da haka, sunadaran inji ne da ke motsawa akai-akai, girgiza, buɗe aljihunsu da rufewa. Molecular dynamics simulation (MD — lissafin kwamfuta na motsi na kwayoyin halitta a tsawon lokaci bisa ga ka'idodin kimiyyar lissafi na Newton) yana sa wannan motsi ya kasance a bayyane: ko aljihun magani yana buɗewa, yadda maye gurbin ke canza sassauci, ko ɗaurin ya kasance barga. AI yana taimakawa wajen tsara saitin MD (zaɓin filin karfi, akwatin ruwa, matakan daidaitawa) da kuma taƙaita sakamakon, amma ingancin jiki na simintin (isasshen lokaci, daidai filin karfi) shine hukunci na ƙwararru. Simulation gajere ko da ba daidai ba yana haifar da sakamako mai bayyana gaske amma maras ma'ana a zahiri.
Tukwici: Kafin amincewa da sakamakon simintin MD, yi tambayoyi guda biyu: shin simulation ɗin ya daɗe sosai (Shin tsarin ya kai ma'auni) kuma yana ba da ɗabi'a iri ɗaya idan aka maimaita (tare da nau'in farawa daban)? Motsi guda ɗaya, taƙaitaccen siminti yana nuna yanayi, ba shaida ba.
Kuskuren gama gari
- Zaton tsarin ya tabbata ba tare da kallon pLDDT ba. Da'awar da aka dogara akan ƙananan wuraren tsaro na yaudara ne.
- Kuskure makin docking azaman ma'aunin kusanci. Maki yana dangi; Yana buƙatar gwaji.
- Kuskure tsayayyen tsari don gaskiya mai ƙarfi. Sunadaran suna motsawa; Tsarin daya ba ya ba da labarin duka.
- Karɓar shawarwari don ƙwayoyin da ba za a iya haɗawa ba. Abubuwan da ake samarwa dole ne su wuce ta hanyar tace sinadarai.
- Tsaro / makanta mai amfani biyu. Ya kamata a ƙi amincewa da buƙatun ƙira masu guba ko masu cutarwa.
a takaice
AlphaFold da docking kayan aikin AI masu ƙarfi ne waɗanda ke haɓaka aikin injiniyan furotin da gano magunguna; Hasashen tsari yana jagorantar hanya, docking nau'ikan dubban kwayoyin halitta, ƙirar ƙira suna ba da shawarar sabbin 'yan takara. Amma fitowar duka ita ce hasashe: karanta ƙimar amincewar pLDDT, kar a yi kuskuren saka maki don kusanci, kar a rikitar da tsayayyen tsari tare da gaskiyar gaske, kuma tabbatar da kowane ɗan takara mai mahimmanci da gwaji. Haɗin kai, aminci da wayar da kan amfani da dual abu ne da ke da mahimmanci a ƙirar ƙwayoyin cuta.
Aikin aikace-aikace
Nemo tsinkayar tsarin don jerin sunadaran da ake samuwa a bainar jama'a daga bayanan AlphaFold (ko sabar kan layi). Bincika taswirar pLDDT kuma raba yankuna masu aminci da masu shakka. Sannan sami sharhin AI akan wurin aiki na wannan furotin kuma kwatanta kowace da'awar da ta yi tare da taswirar pLDDT: shin da'awar ta dogara ne akan yanki mara ƙarfi? Ƙimar sakamakon a cikin sakin layi ɗaya.
jerin abubuwan dubawa
- [] Na kimanta hasashen tsarin tare da ƙimar amincewar pLDDT.
- [ ] Na kauce wa da'awar dangane da ƙananan amincewa yankuna.
- [ ] Na fassara makin docking a matsayin matsayi na dangi, ba cikakkiyar alaƙa ba.
- [ ] Na lura cewa tsayayyen tsari baya wakiltar ɗabi'a mai ƙarfi.
- [ ] Na tace shawarwarin kwayoyin halitta masu amfani ta hanyar hadawa da aminci.
- [ ] Na haɗa kowane tsinkaya mai mahimmanci zuwa tsarin tabbatarwa na gwaji.