PyRx - Virtual Screening Tool | Multiple Ligand Docking | Lecture 42 | Dr. Muhammad Naveed

PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with an easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for structure-based drug design
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.
#PyRx #MultipleLigand #DrugDesign

[@lifesciencewithhussain]

Thanks, Sir you are the only one who I understand and learn much more than what teaches us in university. May Allah bless you with long and prosperous life along with your family.

[@Prof.Dr.MuhammadNaveed]

Glad to hear that

[@surajjoshi3612]

1.Text mining 2. Machine learning model by using random tree classifier 3. X-score software for redocking 4. Drug like profile by faf drug 3 5. Anticancer efficacy by using CDRUG server 6. Median Lethal dose (LD50) of the screened phytochemicals using GUSAR online server 7. Pharmacophores of the screened phytochemicals using pharmaGist webserver 8. UCSF chimera 9. Chemdraw 10. Lig plot+ for protein ligand interaction and Ligprep also Sir please ab pyrx ke baad inko aap bata dijiyega, aapse better koi nahi samjha sakta hai..... You are the super hero for all research scholars.... 😍😍

[@surajjoshi3612]

I am very happy sir now I will get to learn more new things from you..may Allah bless you always and give you a long life

[@Prof.Dr.MuhammadNaveed]

sure dear

[@surajjoshi3612]

1. Identification of plants by text mining 2. Machine learning model development 3. X- score software for redocking 4. Anticancer efficacy for CDRUG online server 5. Pharmacophores of the screened phytochemicals by using PharmaGist online server 6. Drug like profile using Faf Drug 3 server 7. Median Lethal Dose (LD50) of the screened phytochemicals using GUSAR online server 8. UCSF chimera 9. Lig plus+ for ligand protein interaction, and Ligprep Sir inpe bhi bna dijiye videos

[@Prof.Dr.MuhammadNaveed]

noted

[@mohammadabdullah8584]

Thanks for this lecture, your platform is always reliable and quick to understand. Sir kindly clarify that ligands that you are using in Pyrx are 3d (SDF) format or PDB format?

[@sanjaisrao484]

Sir please tell how to enter my xyz coordinates in pyrx for my gridbox

[@Prof.Dr.MuhammadNaveed]

do find from autodock vina or watch my lecture on it

[@sanjaisrao484]

@@Prof.Dr.MuhammadNaveed Sir thanks for replying, U are doing a great job of clarifying doubts in comments,most of them don't do this, So only sir u are the best bioinformatics teacher in youtube Your videos also are not that long , I learned many things from u sir thank you

[@muzamilshah1262]

Salam sir Sir kia hum crude extract ka molecular docking kr sakty hain? Please Bata den torha details mai

[@professorswenson3504]

Don't the ligands need to be prepared such as their charges?

[@johirislam8174]

how can we understand which chain of the protein are optimum for docking. As there are five chain that you have shown in this video and you remove randomly 4 accept chain A

[@anisaaina4067]

Sir really great. Sir kindly tell, how can we dock in the presence of metal in active site? like iron

[@anusharma2074]

Very informative

[@AmirAli-gf1fc]

How i know that the ligand act as agonist or antagonist?

[@job506]

Many thanks. When I wanted to Make Macrolecule, a dialog box on alternte conformation poppoed up and I also got this error: AttributeError: member babel_type not found. What should I do?

[@surajjoshi3612]

I am very happy , thank you so much sir.... Great great

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@madhurjyabiswas6445]

sir many many thanks for this lecture

[@sandhyaupadhyay5634]

sir does pyrx is feasible for metal docking? if so, how can I correct my atom syntax.

[@sumayyaumair5505]

I have question I seen some tutorial they use cmd promat for generation of different poses but u have not use this is it necessary or not please explain

[@madhuripagare7523]

Sir, how to multiple docking in Autodock 4 software?

[@minhajashraf8372]

sir i am facing this issue in pyrx. Traceback (most recent call last): File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\molNavigator.py", line 636, in OnRightUp if hasattr(node.allAtoms[0].assembly, 'lineActor') and node.allAtoms[0].assembly.lineActor.GetVisibility(): File "C:\Program Files (x86)\PyRx\lib\UserList.py", line 31, in __getitem__ def __getitem__(self, i): return self.data[i] IndexError: list index out of range kindly help me

[@roughcooking]

If we want dock 100 molecules thenhow can we select one by one? Solve the issue sir

[@SufyanKhan-qv4js]

AOA sir how are you? Sir, what about if one of our ligand downloaded from PubChem has only a 2D structure and the rest of our ligands of interest has a 3D structure so can we still proceed with docking by pyrx?

[@moazzamaibrahim6716]

Most awaited video, thank you so much sir. 😇

[@Prof.Dr.MuhammadNaveed]

pleasures

[@agurokpondaniel3792]

Is blind docking really good?

[@surajjoshi3612]

Thank you sir, Now please tell me all these techniques, I will be grateful to you for the rest of my life.

[@Prof.Dr.MuhammadNaveed]

sure

[@iqrahasan9114]

kya iske baad bhi docking ka koi step h ya is m final result bhi btaya h aapne

[@Prof.Dr.MuhammadNaveed]

yes on pymol bonds length

[@ajyui847]

I can't save sdf file from the docking results , it saves only 3 , what could be the problem?

[@Prof.Dr.MuhammadNaveed]

do try from drugbank or pubchem

[@rabiadhamyal3586]

Sir can people with Ms industrial biotechnology apply for lectureship in biology???

[@dipanjankarati7208]

Sir, when i am going to load protein then they are showing that "protein.pdbqt file not found in C:\user\karat\mgltools\pyrex\dekstop\macromolecules

[@dipanjankarati7208]

Kindly help me sir

[@birdsworld570]

How to custom set grid in PyRx? It seems automatic

[@haithamal-madhagi7769]

Thanks sir for the tutorial. I am facing a problem related to the inability to open preferences tab (immediately an error is showing). Besides, the receptor cannot be converted to PDBQT, error is showing. Please help me.

[@Prof.Dr.MuhammadNaveed]

working and try again

[@haniabaig6090]

sir kindly tell me how to resolve insufficient memory issue in pyrx?

[@raidanazmul6225]

How to get the ligands or how can I download ligands?

[@dhruvaagarwal2326]

sir i am getting same error as yours that dialog box that opened up. and in last it shows me the error that.pdbqt file not found

[@Prof.Dr.MuhammadNaveed]

check your pdbqt files

[@surajitsarker8950]

Sir your tutorial is indeed very fantastic. But I am facing difficulty since my ligand contains a BORON atom that is not defined within PyRx. Can u guide me how to do the Parameterization of the unknown "Boron" atom in PyRx. It would be very helpful 🙏.

[@Prof.Dr.MuhammadNaveed]

then use Chem draw for this regard, then perform Autodock vina

[@srikamalesh2402]

Hello sir I have a problem to convert the protein to macro molecule it showing error I am using 1US0 pdb help me to rectify my problem thank in advance

[@Prof.Dr.MuhammadNaveed]

check file name o or 0?

[@amarkar11]

Can you tell me how to install pyrx in Ubuntu linux?

[@lfmbysuro]

Namaste. From India, can you sir help me to download this in MacBook?

[@afsanaaz3268]

Thanku so much sir,

[@deepikayande4555]

Sir how to select multiple protein?

[@khaledbhuiyan5159]

Sir please make a video on NGS de novo assembly . Watching ur video from Bangladesh .

[@Prof.Dr.MuhammadNaveed]

noted

[@BioinformaticsWANA]

Thank you sir very informative and helpful. Kindly sir plz make a tutorial on SHesis and plink software as well. How to use that? Thanks

[@Prof.Dr.MuhammadNaveed]

please elaborate these

[@BioinformaticsWANA]

@@Prof.Dr.MuhammadNaveed sir these are biostatistical tools used in genetics

[@fatimanoor5424]

👍..... Sir kindly milsoft docker k bary mey b video bnay inhi Dino mey ...

[@zainiiBee]

Hey are u using molsoft ?

[@fatimanoor5424]

@@zainiiBee No... It's paid software and trying for trial period..

[@fatimanoor5424]

@@zainiiBee No... It's paid software and trying for trial period..

[@Prof.Dr.MuhammadNaveed]

noted

[@muhammadabraryousaf1062]

Dear Sir, Kindly make a video on MOE software

[@Prof.Dr.MuhammadNaveed]

noted

[@surajjoshi3612]

Sir plz next video x- score docking revalidate software pe bana dijiye plz sir

[@Prof.Dr.MuhammadNaveed]

noted

[@surajjoshi3612]

@@Prof.Dr.MuhammadNaveed Sir lecture kb aayega

[@shakilcuchem]

From bangladesh

[@Prof.Dr.MuhammadNaveed]

welcome

[@markadu7204]

can you speak English?. Your presentation is good but you are only speaking to those that understand your language. At least let there be a subtitle.

[@Prof.Dr.MuhammadNaveed]

will share lectures in English in near future

[@carinapeters440]

Lol its just docking not virtual secrening

[@Prof.Dr.MuhammadNaveed]

both