MOE Molecular Docking Analysis | Complete guide for Beginners | Lecture 83 | Dr. Muhammad Naveed
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- Опубликовано: 11 сен 2024
- MOE Molecular Docking Analysis
Download link: www.chemcomp.c...
COMPUTER-AIDED MOLECULAR DESIGN
CCG is a leading developer and provider of Molecular Modeling, Simulations and Machine Learning software to Pharmaceutical and Biotechnology companies as well as Academic institutions throughout the world. CCG continuously develops new technologies with its team of mathematicians, scientists and software engineers and through scientific collaborations with customers.
This will focus on fragment-based drug design tools in MOE. Combinatorial fragment design and scaffold replacement in the receptor active site will be covered in detail, along with approaches for fragment linking and growing. A method for generating a series of closely related derivatives through medicinal chemistry transformations will also be presented. Finally, the use of pharmacophores and 2D/3D descriptors to guide drug design processes will be discussed.
CCG maintains a permanent team of scientists, mathematicians and software engineers engaged in a continuous program of research and development in Computer-Aided Molecular Design, Informatics and Computational Chemistry and Biology.
This covers MOE applications for interactive structure based design. Examples include active site visualization, protein-ligand contact analysis and ligand modification/optimization in the receptor pocket. Use of the docking module and its application to assess ligand flexibility will be discussed. A protocol for aligning and superposing protein complexes in the context of protein selectivity will be studied.
An automated approach to summarize pocket shapes and binding hot-spots from a collection of protein structures is presented. Pocket shapes are described using pocket volumes derived from Alpha Sites and molecular surfaces. Binding hot-spots are located using pharmacophore features generated by AutoPH4. Collections of pocket volumes and pharmacophores are analyzed using feature densities which map onto a universal grid the fraction of structures that possess a given feature at each point in space. Regions with high pharmacophore feature densities identify the most persistent interaction binding hot-spots over the collection of structures. Pocket volume densities detect and classify binding site regions into core pockets and sub-pocket regions. Fingerprints that represent pocket shape, sub-pocket presence and pharmacophore feature presence are derived and used to cluster and classify multiple protein structures using standard fingerprint clustering tools. Application of the method to fragment-based drug design, minor pocket detection, selectivity mapping, binding-mode classification and custom docking scoring function creation is presented.
About Dr. Muhammad Naveed
(HoD, Biotechnology, University of Central Punjab, Lahore)
With distinction, Dr. Muhammad Naveed obtained a Ph.D. degree in Biotechnology (Genomics & Bioinformatics) from Quaid-e-Azam University, Islamabad. He has won Ph.D. indigenous & IRSIP scholarships from HEC. He has done Pre-Doc research at the University of Ghent, Belgium. HEC awarded him the best Ph.D. (IRSIP) Scholar of the year in 2013 & QAU honored him as a “Distinguished Alumni” in 2017. He is doing research projects in Bioinformatics, Molecular Biotechnology & Vaccine designing, and Drug designing against infectious diseases. He has supervised 70 MSc. and 60 MPhil. & 01 Ph.D. students. He has published 112 Research articles with 604 impact factors, 2000 citations, 01 book, and 03 book chapters. He was awarded the distinguished “Researcher of the Year” in 2016 (UoG) and 2018, 2019 & 2021 (UCP).
#moe #docking #drugdevelopment
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Does it a free offline software. Because when I get into the MOE page for download it showed two option one for trial and the second one for download MOE for existing customers and evaluators. So how can i install it for ,lifetime.
very nice explanation without wasting time you have taught in a very impressive way. The video is specially useful for beginners. Thanks from SWEDEN
Thank you sir waiting for this video for a long era
glades its helped you
sir my question was that some drug molecules inhibit the target site and some drug molecules activate the target site, why does this happen?
When we talk about corona virus, when we dock or give any drug molecule to us, then it gets blocked, why does this happen sir, it can also happen that these drug molecules can increase or do well expression. I do not understand that where we get the benefit, we say that this drug activates the mutated target site (RTK or insulin receptor) or its expression is large, or some drug molecule target site like spike protein that is inactivating....
yes its depend on receptor cite and further after binding change physiochemical nature of compound
@@Prof.Dr.MuhammadNaveed how we will validate?
If we use single strand DNA only as receptor. We have to choose protein option or another. If yes then results will be ok?
i like the way you explained the complex process very easily , love from INDIA ❤
prepare tutorial on how to sketch 3d structure of organometallic compounds (example-ferrocene) and their docking
many thanks
pleasures
how to download docked complex of specific pose after docking?
Well done Dr Sab appreciated work. Please I request you to upload lectures on DnaSP and eBURST software and how they work in Multi locus sequence typing
sure and noted
@@Prof.Dr.MuhammadNaveed thanks a lot its much helpful
Thanx sir
Ligand sdf library need to prepare and minimization before run or not ?
Great lecture. Sir mn docking pa research kr rhe hun kindly suitable title suggest kry .kis proteins pa work krna chahye .plz guide me
I couldn't download this software. how can I use this for my working?
hello sir i published a paper using moe and now moe assistant manager is asking for license number. please help me
its mean autodock vina result is not good? i have used autodock for my research
سلام علیکم
Respected Sir
I need your help because I tried to find the ligand interaction but it comes blank please help and explain
Aslam o Alikum sir how moe download it with license or trial ?
Results will effected by paid or trail or not
Sir plz help me how to download it i can't download it
Thank you Sir. Could you tell me Don't need '' energy minimize" for protein and ligan?
REALLY GOOD SIR
Download pe click krne k baad options atay hain request type usme se kisko select krna hai?
Thank you very much very informative
Sir plz teach how to design different types of molecular markers
sure but explain your query in detail
Asslam u Alikum sir.sir Kai hum B's master bioinformatics karny ka bad apni pharmacy bana sekhty hai ???ye fir MPhil biotechnology ka bad pharmacy bana sekhty hai piz guide me sir.???
waslam ca do after Biochemistry degree
Very informative, how can we draw 3d structure here in moe
Sir please make a video on multiple epitope vaccine designing
already shared so watch from my channel
Plz prepare lecture about protein protein interaction
Thanks for the wonderful video. I've done docking for a series of GPCR with their native ligands using MOE. Unfortunately, the obtained affinity and rmsd aee not reproducible. I did as below:
First I downloaded a pdb file. Removed all unwanted compounds and water molecules. In presence of the native ligand I did a quickprep. Finally docking (by default parameters).
Could you please help me with my problem?
By the way I saw in some video, some people do minimization before quickprep. Do you suggest it?
then try with autodock vina
Best
glad it helps you
Sir how select ligand and receptor?
Aoa, can you send the crack version link of moe as I'm doing my project and i need it badly😢
Very informative 👍
glads its helps you
Great sir
pleasures
Sir MOE open nhi horhe licences manages rhe hn
use crack version
@@Prof.Dr.MuhammadNaveed ok sir. Sir ap es online training start kry tu...
I need it's crack version , please if any one have
It will be interesting
sure
Wish you were demonstrating in English ..
How to download moe software sir please help me
Ib to me❤
How to view protein protein interactions after protein protein docking on MOE!?
use pymol
Sir could you please let us know that how we may access/download MOE. They are asking for licensing validation even for academic use. Could you please guide or provide access to MOE. It will be a huge help. JazakAllah
use crack version
Replay to this email for the full version of MOE free crack version
@@Prof.Dr.MuhammadNaveed where to get the crack v for MacBook?
@@Prof.Dr.MuhammadNaveed Janab poori instructions dya karen video me hi... :)
Dear Faizan from where?
You should talk in english....
There are many non indian people try to learn also
Anyone else who download it plz help me
crack version