Protein DataBank (PDB) | Protein Structure and Function Properties | Lecture 7 | Dr. Muhammad Naveed

PDB Protein Databank Homepage & Complete Detail
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology.
#PDB #3DStructure #structuralBiology

[@iqrajaved4620]

Veey informative..thank you sir

[@hafizhusnain6153]

Good job

[@studentschannel7234]

Masha Allah Sir
I learn much from your channel

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@umbernoreen7983]

Me too

[@maheshswami5226]

I fill pleasure to your work

[@Prof.Dr.MuhammadNaveed]

Welcome

[@preetichauhan2812]

Informative lecture! Thank you sir

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@umbernoreen7983]

Studio visulizer kasy download krty....quick down load ni ho raha...ap boht fast lecture deliver krty...speed kuch km rakhyn.....docking k liy protein structure download ni howa

[@stephenmburu1872]

While performing a BLASTp search with protein sequence against the PDB-
database you have one hit with low E-value and two hits with somewhat
higher E-value. On inspection of the PDB file with the best score it turns out
that this 3D structure has a rather bad resolution and misses coordinates of two
loops. Describe how you can use this information to identify your protein?

[@Prof.Dr.MuhammadNaveed]

use sequence with low E-value and for structure validation watch my today lecture

[@adnanrahman8326]

Sir if you arrange a paid workshop for us it will be better for us about NGS. reverse vaccinology, Sanger sequence analysis

[@muzix9955]

that "thank you" goes through my heart 😅

[@Prof.Dr.MuhammadNaveed]

pleasures

[@muzix9955]

thanks sir, your effort is a lots for us before the day of exam

[@khawajaasadhusnain7849]

Thanks alot Dear Sir

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@lifesciencedecoded]

Sir can we docked multiple target site for single disease with one ligand ?
Sir jese humne, suppose X naam ke target site ko dock kiya A naam ke ligand se, or result -12 aaya. Phir humne y naam ke target site ko dock kiya A naam ke ligand se , or result -10 aaya . Phir sir kya hum phir A naam waale ligand ki help se docking kar sakte hain wo bhi ek saath ?
Agar kar sakte hain to kese kar sakte hain (multi target site docking for a single disease with the help of single ligand)
Or agar nahi kar sakte hain to kyu ?
Sir doubt clear kar dijiye

[@Prof.Dr.MuhammadNaveed]

yes

[@alijaffarrazaalijaffarraza5182]

Thanks Sir Jee

[@santoshvyas2955]

thank u sir

[@rabiajahangir6415]

Salam. I didn't get the nucleotide sequence of pdb I'd 5vf9. .could u help me plz

[@Passiontoserve]

Keep up the good work 😃

[@Prof.Dr.MuhammadNaveed]

sure

[@whatsnew14]

How to find out pdb I'd ?
Protein name hai fasta structure hai ab ushe particular protein ki pdb I'd kase find out kare ?

[@Prof.Dr.MuhammadNaveed]

write protien name on Protein data bank then show you ID

[@jozabatool3663]

Your lecture was too Informative..
But, sir I have a question that how we get the id of protein to enter in pdb? where that IDs are available?

[@Prof.Dr.MuhammadNaveed]

on PDB or from google search by protein name

[@jozabatool3663]

@@Prof.Dr.MuhammadNaveed ok sir thanks

[@Asmat0168]

sir hmain ksy pta chly ga k pdb mn ab tk kisi b strain k ktny protein report hoay or regulator ktny ha?

[@Prof.Dr.MuhammadNaveed]

By search with strain name

[@somiasumbal4622]

Where's results description of ProtScale primary structure prediction kindly share the link

[@Prof.Dr.MuhammadNaveed]

watch lecture on expasy translator

[@piyalimukherjee1502]

sir from where you get PDBID?

[@nain9038]

Assalam o alikom sir.....sir plzzzzzzz chimera par aik vedio bana de plzzz

[@Prof.Dr.MuhammadNaveed]

waslam sure

[@nain9038]

Sir plz koi hint dyde k ye q save nhi ho rhi pdb form mai file sara process kar lyte hai but end mai file save ni hoti🥺🥺🥺

[@Prof.Dr.MuhammadNaveed]

file save hu g hu but need to install pymol or other visualizer to view

[@maheshswami5226]

Sir please amino acid substitution matrix par video banaye

[@Prof.Dr.MuhammadNaveed]

sure

[@maheshswami5226]

@@Prof.Dr.MuhammadNaveed thanks sir

[@nain9038]

Sir mai research student ho...mjy aik issue hai k chimera mai file pdb form mai save nhi ho rhi sir plzzz koi solution bta de plzzz🥺🥺🥺🥺🥺

[@Prof.Dr.MuhammadNaveed]

watch my lecture on drug design where have some part on chimera

[@shakeelasghar3341]

Sir Mera protein creatinine ratio 27.7 hai hum is ko mazeed bahter kese kar sakte hein

[@Prof.Dr.MuhammadNaveed]

ratio for what?

[@shakeelasghar3341]

@@Prof.Dr.MuhammadNaveed 0.20

[@ehsam_uddin]

plz mention pdb reader link

[@Prof.Dr.MuhammadNaveed]

do check on web

[@muhammadabraryousaf1062]

How to get PBD id for a specific protein

[@Prof.Dr.MuhammadNaveed]

If this protein already submitted and available on PDB then use that ID or if newly identified and characterized protein then do submit it on PDB and they issued ID within a month

[@muhammadabraryousaf1062]

@@Prof.Dr.MuhammadNaveed Thank you so much sir

[@sharmashiv]

Hello sir

[@Prof.Dr.MuhammadNaveed]

yes dear

[@sharmashiv]

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