Ramachandran Plot | PROCHECK | Protein Secondary Structure Validation | Lec 22 | Dr. Muhammad Naveed

The Ramachandran plot is a plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in a peptide. ... By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.
This video is about Ramachandran Plot Assesment.
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.

[@zainiiBee]

THANK YOU SIR, really helpful,, I am a student in Qatar and found this very helpful. I have done Ab-initio modelling through I-Tasser and Robetta both showed diff models. Now i want to validate and in my Ramachandran plot Most favoured residues are 85.8% and additional allowed residues are 9.9% and dis-allowed is 2.1%. is my structure valid or not? also for Ab-Initio modelling, I-Tasser or Robetta which is good?

[@Prof.Dr.MuhammadNaveed]

Not good but you can use it for further predication

[@zainiiBee]

@@Prof.Dr.MuhammadNaveed Thank U for ur reply Sir. Can u suggest me a good step which tool or server should i use?

[@duafatima6283]

Hi there, how did you get the percentage btw i am not using procheck..

[@ramneetkaur2500]

Excellent lecture. Very clear.

[@Prof.Dr.MuhammadNaveed]

Glad it was helpful!

[@muhammadmuzammal1144]

Jazak Allah❤

[@Prof.Dr.MuhammadNaveed]

pleasures

[@lifesciencedecoded]

Sir kya aap ek animation video create kar sakte ho drug design pe... Disease Target identification Protein sequence Structural determination Protein intrinsic disorder Searching and screening of ligand Select drug candidate Clinical trial Drug design

[@Prof.Dr.MuhammadNaveed]

noted and will do soon

[@tabishkhokhar4597]

❤

[@realsanafatima]

Jazak Allahu khair sir well explained

[@Prof.Dr.MuhammadNaveed]

Glad to hear that

[@muhammadbilal7091]

Well explained!

[@Prof.Dr.MuhammadNaveed]

welcome dear

[@bipinkb8606]

Thank you so much for this awesome video sir, some pdb files while I upload to "Galaxy refine", it is showing like 'there is a break in a protein chain'. How to avoid this error sir.

[@SamiraSadeghi-]

the link and prochek is unavailable now, what should I do?

[@Prof.Dr.MuhammadNaveed]

do use ERRAT

[@zainiiBee]

sir , after refining my G factor in summary profile is 0.26, while everything else is in good region like 90.9% in most favoured and 9.9 in allowed region and no dis-allowed. the G factor is not negative, should i consider my model good or not?

[@Prof.Dr.MuhammadNaveed]

yes go ahead

[@sanariaz2809]

Sir please Bata Dain k summary file mein G factor negative mein ana chaiyae ? Mein model ko 3 bar refine Kar chuki Hun laken G factor negative ni arah

[@Prof.Dr.MuhammadNaveed]

its ok then proceed further

[@mimimania1723]

jazakallah khair

[@SufyanKhan-qv4js]

AOA sir how are you? Sir, I have generated a model of SARS-CoV 2 E-protein by modeller and have validated the the model by ERRAT and PROCHECK but I'm bit confused. Sir, the overall quality factor of the model by ERRAT is 63% while the PROCHECK Ramachandran Plot depicts the 94.4% of the residues are in the most favoured region, 4.2% residues are in additionally allowed region, 1.4% residues are in generously allowed region and no residues are in the disallowed region so can I use this model for further analysis such as docking? Thank You!

[@Prof.Dr.MuhammadNaveed]

do proceed on the basis of rama score

[@RidaTabasam]

Sir protein ka sequence kysy lyna hay

[@fahimalamnobel4789]

plz make a video by Rampage server

[@Prof.Dr.MuhammadNaveed]

Dear RC plot is best than RAMPAGE as most cited one so follow this for your predictions

[@lovelygupta3896]

Incase around 85% residues are in favoured region. Can we consider that protein structure for docking?

[@Prof.Dr.MuhammadNaveed]

yup but refine further by Glaxyrefine watch my lecture on it

[@mussaratshaheen3412]

Respected Sir,,,, Why there is no Pakistani who developed bioinformatic software,,,, we always have Indian or other foreign people who developed these software,,,,,

[@Prof.Dr.MuhammadNaveed]

Agreed as IT-based knowledge is well developed in India but very soon you will see Pakistani names in this list as day by day many working on new tools

[@drabhishekpathak4389]

Most favored residues are 89.5% and additional allowed residues are 8.7% and dis-allowed is 0.9%. is my structure valid or not? when I m going to submit in PMDB its show "Non-proteic moiety present in your file" can u explain how to resolve it and submit in PMDB

[@Prof.Dr.MuhammadNaveed]

yes seem ok but do refine by Glaxyrefine then submit

[@atialiaqat7012]

Sir I got 78.1% in most favoured region nd 0.4% in disallowed region. Can I use this structure furthur?

[@Prof.Dr.MuhammadNaveed]

can do but good score is more than 85% and can use but verify with other tools as well

[@kook9182]

Which is the disallowed region? Please help

[@Prof.Dr.MuhammadNaveed]

this lower last mentioned in lecture

[@sarahnawaz6925]

can it help validate structures determined by I TASSER

[@Prof.Dr.MuhammadNaveed]

yes

[@archanabhati111]

Sir, 89.1% for Ramachandran plot could be used further??

[@Prof.Dr.MuhammadNaveed]

yes can be considered for further refining

[@archanabhati111]

@@Prof.Dr.MuhammadNaveed i got this score after using Galaxy refine... is there any other tool to improve my structure

[@ramandewanganrdhesir2694]

Sir please send url