Ligand Selection & Preparation for Drug Design | CADD Step 1 | Lecture 33 | Dr. Muhammad Naveed
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- Опубликовано: 25 авг 2024
- e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: bioinfo.ipmc.cn....
About Dr. Muhammad Naveed
Dr. Muhammad Naveed obtained PhD degree in Biotechnology (Genomics & Bioinformatics) from QAU, Islamabad with distinction. He has won PhD indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research from University of Ghent, Belgium. HEC awarded best PhD (IRSIP) Scholar of the year 2013 & QAU honoured him as “Distinguished Alumni” in 2017. He is doing research in Bioinformatics & Molecular Biotechnology. He has supervised 25 MSc., 30 MPhil. & 01 PhDs. He has published 51 research articles, 01 book and 03 book chapters. He has been awarded distinguished “Researcher of the Years (2016, 2018 & 2019)” by UoG and UCP.
#CADD #eLEA3D #LigandPreparation
Your lectures are the best lectures in Pakistani RUclipsrs.
JazakAllah
Thanks, Dr. Naveed for your great work. Your lectures are very clear.
Thanks for liking
Kudos! Prof. Naveed Sir👍
Thanks a ton
Thanks a lot sir. Your videos are truly helpful. God bless
Thanks and welcome
Thanku so much sir ,
pleasures
Thanku so much sir😍😍
welcome
Tnxxxxxx sir
welcome
sir apne edr ek he protein structure upload kia tha, jeske api discovery studio py purificantion ke,,, ab elea3d py slection kafe sari ligands k drmayan hote hy,,,, ye ligands kaha se agay. ?
great work sir
thanks
Sir, we added the receptors but please let me know where to add the ligands. And email for results?
Please let me know. Thanking in anticipation
Sir I am using auto dock vina but in my case xyz axis are not coming for my protien on auto dock vina
w8ing sir
pleasures
Very informative video sir👌
Thanks and welcome
Sir how to interact non ionic surfactant with anti drug
Conjugation. Is it docking or any other techniques
Sir I am unable to get the main could you please tell me how can I get mail for the drugs
Aoa.. sir yeh apny receptor kis base py lea ACE2 ka.. jb hm NCBI py search krty hain aur uniprot py vhan ACE2 ka sequence length 805 hai aur yeh jo apny protein li hai iska sequence length 605 bta raha hai PDB. ab jb mainy check kea BLAST k through bhe to iski koe complete structure pdb main nhein hai ek hai structure lekin uski 601 sy 660 main single AA ka change hai jesay apsy he seekha vh bhe krna.. to agar ap bta dein tu thankful hounge...
yes it varies due to partial gene sequence and you may use which mentioned in literature
Sir you hadn't fill the binding site details so it's not working...
that come from autodock vina
Sir Mera project hai i am Biotechnolgy student r mai na sars2 cov 19 hi chose kiya for drug designing mai na wesy hi kiya vedio Daikh k but result visuliz nhi ho rahy
Sir ya apna protein drug discovery btai hai pdb sa kindly guide me how can we design drug of gene related diseases
Sir ye cadd course kitne lectures pe complete ho jaayega , jisse hum easily sab kuch detail main docking karna sikh le....
4 lectures from 33 to 36
If my best score is 32 is it good to go for further steps
sir it shows Bad character in your data when file is uploaded pl advice
Asslam o Alaikum sir hum ny apny ya result ppt pa lgany ho tw Kesy lgay gy bcz structure download mai show nhi ho raha r result bhi tw hum ppt Kesy bnay gy?
Sir, please make a video on Virtual screening using "Lea3D" and "mtiopenscreen"
sure
@@Prof.Dr.MuhammadNaveed thanks a lot Sir
Sir! Hm NCIB sa sequence La k through I Tasser protein k structure download kr k by using ELEA3D can we find out ligand, if we have no idea about receptor, only known protein structure.
yes can do
AoA Sir! How can we find protein PDB ID ? I want to find for LRRC-15
very informative video sir ......thank you so much
sir i have a question regarding receptor selection ...pls tell me how to decide which receptor i should chose and what is the parameter to select the receptor in drug designing
Can someone help me, how do I determine the final weight score? Sir said its from 1-9 but I am really clueless on how to decide the value. Will you please help me sir or anyone?
Aoa.. sir can you please tell why we are finding inhibitor against ACE2 although its a receptor in our body and it has its own role. If we inhibit ACE2 will it not cause disturbance for other functions. e.g if i wanna work on HIV for HIV in our body receptor is CD4 if we inhibit this receptor, it cause hinderence in proper functioning of body if we apply same procedure on it or give some suggestion if possinble, Waiting for your kind response thankyou.
yes some how but after that we can check the toxicity analysis
Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga.....
in nature many thing happened thats why we go for control conditions
Sir isme humne protein to select ki , but ligend automatically show honge kya after complete docking ? Plz sir solve the doubt
yes
Sir
Error could not open conf.tct for reading show ho raha hain last step m
do make file as shown in video then put all in vina folder in C derive
Sir ye jo tool hai voh free hai?
At LEA3D, when we upload modified target files and provide x,Y and Z parameter. Shall we opt de nova or virtual screening in option.
virtual screening or default
@@Prof.Dr.MuhammadNaveed
Ahhh , than I did mistake...I opted for de nova.
I still got the results...I followed your instructions just in choosing the opted by mistake I opted than de Nova
@@jyotibala102 on which basis you selected no. of atoms after selecting de novo design
@@fatimazulfiqar6751 I used default parameters...by mistake i used de nova..Dr Naveed has shown virtual screening demonstration.
Thanku sir , first time maine docking ki with the help of patch dock, credit goes to you sir , aapki video se hi sikha..... Sir but result ko kese analysis kare ye samaj nahi aa raha hai , plz help me sir.....
watch results interpretation and interactions my PyMol
@@Prof.Dr.MuhammadNaveed thank you sir , doing great work....
Waiting your next cadd lecture video in detail....
Sir kya hum is cadd course ki help se phir koi bhi known docking ko perform kar sakte hain.....
yup
A.o.a how could we find the name of the ligand we have designed
on the base of receptor binding site
@@Prof.Dr.MuhammadNaveed can you sir please explain as I am working on nucleocapsid protein of covid 19 and I l have applied lea3d and got 21 ligands but unable to find their names .. in the next step you used Swiss target prediction on human ace2 receptor but my protein for which I have find ligands was nucleocapsid protein
Thankyou Dr Naveed..Nice information. Plz can you suggest how we may change discover file to PDB as its showing error when we are uploading at eLEA3D
we cant change that protein structure but yes you can pick any other similar protein of same group
@@Prof.Dr.MuhammadNaveed actually I did that tomm, while saving the I changed format...I done my analysis too using that file ..Thankyou
Sir kindly suggest a research topic regarding drug designing
any disease
How to provide email Id, in the server page there is no option as such. Then how to get result in my mail????????????
check home page
How can I open pdb file???
Use discovery studio or pymol
How do i creat virtual library for screening???
literature
Sir! Breast Cancer k liye drug design krna hu ligand find out krny k liye hm breast causing cancer protein k structure use kryn gy .....ya receptor find out krna pry ga for ligand
both
Sir! How much time is required to lea3d for giving result???
15 hours had passed but I didn't get result.
some time 2-3 days or do run again
Oh god
Hi. I am Waqas, I am a biotechnology student.I am learning bioinformatics dues to its unique features and that it gives more opporunities to explore living systems at atomic and molecular level without need of expensive equipments. I request you to knidly explain from programming point of view also .. I know python and i use linux.. but there is no proper guidance for how to use programming in bioinformatics.
Thank you
Waqas.
sure and noted dear
Sir plz tell after first submission it moves to next page where it want email so i put but sir after that it gives the 3 option of option scaffold and also next 2 ones so what to do
do proceed accordingly
sir how i find the cordinates of the center binding sites. Suppose i choose a receptor from another visrus .So i have to do docking after the ligand prediction. But how i do docking before that??
by autodock vina
ligand name? from where we get from the result.........or is it de nova ?
no dear this ligand come on the base of target receptor interaction homology but you can go for de novo as well and its name and formula will clear in step2 after similarity search and hits
@@Prof.Dr.MuhammadNaveed oh ok...Got Dr Naved...Hopefully in upcoming video you may demonstrate that too. THANKS A lot
Sir maine saare stepwise perform kiya , but last time main vina(764kb) open hi nahi hora hai , window mera 8.1 hai sir.... Plz help me sir...
reinstall it
Sir koi book recommend kijiye jo ligend /phytochemical based ho....
go for online tool ligandbook
I did the same steps but in results i did not received population means score. plz guide
if your receptor score is grater than 1 then it give population score so try to use other version of receptor form PDB
@@Prof.Dr.MuhammadNaveed Thnx
Sir eLea3D main protein fill kiya , uske baad grid values bhi input ki , phir weight in final score 1 kiya phir submit kiya to ye show hora hai..
Bad character in your data ACE2 protein.pdb, please complete the form. Press backword on your browser....
Naa hi email ko fill karne ke liye koi option aaya
change protein then do again