ClusPro | Protein-Protein Docking | Protein-Protein Interactions | Lecture 25 | Dr. Muhammad Naveed

The ClusPro server (cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank format. ... Six different energy functions can be used depending on the type of proteins
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.
#ClusPro #ProteinDocking #InteractionAnalysis

[@fatimanoor5424]

Thanks Sir... Apka HR lecture helpful hy.. Allah pak ap k liy asania pyda kry... Ameen

[@Prof.Dr.MuhammadNaveed]

ameen and welcome dear

[@SamiUllah-bx8mi]

Aslamualikum Sir! Please provide a lecture on Protein-DNA docking. How to construct DNA structure for docking , which tools can be used for this and which type of files are required.

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@user-qe4vm6eh5o]

what if our receptor has two chains ? how to write it in chain portion?

[@biswanathtrivedi1141]

Sir, you are my saviour in bioinformatics.. can u make a lecture series on chimeric protein construction (eg: immunotoxins)?

[@Prof.Dr.MuhammadNaveed]

welcome and elaborate or mentioned all tools series here and will do

[@theshillonggirl]

thank you very much for clearly explaining, please also could you explain little more about the interaction interpretation in pymol between two proteins

[@Prof.Dr.MuhammadNaveed]

watch my lecture on PyMol

[@dr.rimshariaz4688]

Sir cluspro se ki gai PPI k interfaced aa kese find kr skty hm. Bonding type and strength?

[@Prof.Dr.MuhammadNaveed]

compare with literature reported bond types

[@sherazbaloch1642]

Nice sir

[@Prof.Dr.MuhammadNaveed]

WELCOME

[@anandraj-he2qb]

Sir can we dock multiple proteins by cluspro

[@saadsalamat3783]

Assalam o Alaikum Sir... sir please add a video on hex tool where u show ligand sites and active sites of a certain protein....

[@Prof.Dr.MuhammadNaveed]

Sure and noted

[@samarpitadash6314]

Sir after doing clus Pro I did ligplot no bonding is showing what I need to do?

[@Prof.Dr.MuhammadNaveed]

go to pymol for visualization of complex

[@aqsahussain1518]

if we dont have any comparative structures so how can we validate our results

[@Prof.Dr.MuhammadNaveed]

there must be any template for every compound

[@farahbalochh4587]

@Prof.Dr.Muhammad Naveed same issue no comparative structure available What to do

[@bhagatsingh6345]

sir good morning. dear sir haw to design siRNA . sir is pe koi lecture .

[@Prof.Dr.MuhammadNaveed]

sure and noted

[@Jun_kki]

Sir, could you please suggest a way by which i can so multiple protein protein docking at once as i want to dock different proteins with one protein.

[@Prof.Dr.MuhammadNaveed]

can try pyrx

[@SufyanKhan-qv4js]

Hello sir very informative video. Sir, I want to dock wild-type and mutant RBD of Omicron Spike protein with ACE 2 receptor by cluspro. How can I do that? Please kindly ASAP. Thank you! Sir, also I have a macromolecule ligand 2s albumin and a model ligand flocculating protein and want to dock it with the mutant RBD Omiron S-protein-ACE 2 complex. How can I do that?

[@ghanashyammahanta1091]

Sir can you please say which residue of one protein is interacting with which residues of other protein...?

[@Prof.Dr.MuhammadNaveed]

look residue numbers

[@fadybaselious4154]

Why is the title and all comments are in English while the video itself is with different language

[@Prof.Dr.MuhammadNaveed]

because these term not be written in native language

[@garimasingh1480]

How can we mention interacting residues of template to the other protein once all this is done. Please reply

[@Prof.Dr.MuhammadNaveed]

use docked complex in PyMol

[@dr.rimshariaz4688]

Aoa... Sir i want to ask that which tool is best for finding interfaced residues in docked complex. Pdbepisa/pdbsum?

[@Prof.Dr.MuhammadNaveed]

pdbsum or pymol

[@gauravkumar747]

Hello Sir. I tried protein-protein docking by ClusPro. But I got the results having chain A only although I uploaded separate Receptor and Ligand PDB files. Please help so that I can do the docking. As I said, only chain A is visible because ClusPro is "joining" the receptor and ligand pdb files.

[@Prof.Dr.MuhammadNaveed]

your selection of chains is not right, so select all chains

[@gauravkumar747]

@@Prof.Dr.MuhammadNaveed sir my protein us having one chain only. So I am selecting chain A in both receptor and ligand. Even then jt js the same result.

[@sanabkhattak427]

Sir Please Make a vedio on Haddock web sever

[@Prof.Dr.MuhammadNaveed]

noted dear

[@sanabkhattak427]

@@Prof.Dr.MuhammadNaveed because most of the W categories research publication use Haddock

[@mairafatima1841]

Sir, i have been seeing an issue while docking my protein's structure with another protein,, as my protein's pbd file not available in pdb so i made predicted file from I-TASSER, and then docked them.... but on cluspro in results the pictures shown there, LISENCE EXPIRED have been written them.... ?? what is the cause behind it.... are my structures docked or not.... ? pls suggest wat to do.... @Dr.kzbin.info/door/sJoOHMFN76fodWMZerEHjQ

[@abdulrazaq9541]

Any tool for site specific protein-protein docking?

[@Prof.Dr.MuhammadNaveed]

patchdoc

[@mohammednashith3037]

assalamualaikum alikum how to find the binding energy for the docking

[@Prof.Dr.MuhammadNaveed]

In docked complex

[@mohammednashith3037]

@@Prof.Dr.MuhammadNaveed is it a software pls brief on it i am a collage student nd i am using it in my project

[@dianaa.valencia3910]

@@mohammednashith3037 Have you solved the question?

[@mohammednashith3037]

@@dianaa.valencia3910 no