I am doing ab initio modelling and I used ITasser and Robetta server. Both showed complete different structures. Now what to do? How to go for valid model. Please guide me
Actually there is this value called RMSD ( Root Mean Square Deviation ) which is PRONE to error. It tells us about the DISTANCE between the atoms/particle/amino acids etc. For minimizing the error , they recently introduced TM-score which gives us structural similarity. It judges the quality of structural template. In this TM scheme, small distance/gap is valued more than the bigger distance as bigger distance results in erroneous value. TM-score GREATER THAN 0.5 indicates a model of correct topology and a TM-score LESS THAN 0.17 indicates a random similarity. Hope this is helpful.
@@frqlectures5970 thank you so much for such a great explanation... I had another question... Can you please tell how this pairwise similarity in TM-align can be put in a network while trying to create a structure similarly network?
@@alennalima3117 There is this maintenance period going on there due to which new jobs cannot be submitted, and already-submitted jobs are running slower than usual. Just wait for few days Alenna . Cheers
Proteins are by far the MOST structurally complex & functionally sophisticated molecules known.The Shape of a Protein is Specified by Its Amino Acid Sequence. It can vary specie to specie. We can see the difference by analyzing the different protein models visually.
@@ahmedawan5909 There is this concept of HOMOLOGY. If there is one hundred percent amino acid sequence identity, then the proteins are identical. BUT many identical proteins have Isoforms due to PTM ( Post-Translational Modifications ) ,DIFFERENTIAL splicing and so on. Their identity will have to be evaluated on a case-by-case basis. If you compare protein sequence across species, you will find sequences that are similar. They are not identical proteins ( strictly speaking). They are homologous proteins that perform the same function in a different species. However, more distant species will have more variable sequences.
Its the Confidence Score. The higher the conf.score- the greater the confidence in the answer. For instance, in the case of I-Tasser's secondary structure prediction of protein, higher number/digit i.e 9 means that the predicted structure is dependable/reliable and if the number is close to zero than we can't really rely on such prediction. In other words it could be erroneous.
Explanation was quite simple..Well done
Loved Your Voice Man!! Excellent work.. Thumbs up FRQ
Thank you for the explanation, sir! I understood it very much.
keep going really enjoyed your vedio and learnt something
Glad it was helpful :)
Very well explained, sir. Thank you very much, sir
I am doing ab initio modelling and I used ITasser and Robetta server. Both showed complete different structures. Now what to do? How to go for valid model. Please guide me
Nicely explained!
I have few questions about using DALI
Thanks bro..👍
Thank You for appreciation, I.Zulfiqar
YOU DESERVE THAT ... 😊
Can you please explain TM-align structure similarity network?
Actually there is this value called RMSD ( Root Mean Square Deviation ) which is PRONE to error. It tells us about the DISTANCE between the atoms/particle/amino acids etc. For minimizing the error , they recently introduced TM-score which gives us structural similarity. It judges the quality of structural template. In this TM scheme, small distance/gap is valued more than the bigger distance as bigger distance results in erroneous value. TM-score GREATER THAN 0.5 indicates a model of correct topology and a TM-score LESS THAN 0.17 indicates a random similarity. Hope this is helpful.
@@frqlectures5970 thank you so much for such a great explanation... I had another question... Can you please tell how this pairwise similarity in TM-align can be put in a network while trying to create a structure similarly network?
Which software or drawing tool you use to mark /underline, please tell sir ji
Its just an extension. "Chrome Extension" to be exact.. You can Google it easily.. Hope this helps ..Cheers :)
there is no Seq submission option on the site??
You just have to place the seq. in the box and then hit I-Tasser button/tab at the left bottom portion of the web.
@@frqlectures5970 Doesn't exist this button/tab of submission in the site. What I have to do now?
@@alennalima3117 There is this maintenance period going on there due to which new jobs cannot be submitted, and already-submitted jobs are running slower than usual. Just wait for few days Alenna . Cheers
The C-I-TASSER works similar like the I-TASSER?
The limit of seq. is a bit shorter there i.e (10, 750) otherwise its ok to use it as alternate. hope this helps.
@@frqlectures5970 thank you so much!
@@alennalima3117 as an alternate , you can also try this tool "PSIPRED". ruclips.net/video/qMas5ZMKHqA/видео.html&ab_channel=FRQLectures
How we can estimated that protein models are different or same in different species?
Proteins are by far the MOST structurally complex & functionally sophisticated molecules known.The Shape of a Protein is Specified by Its Amino Acid Sequence. It can vary specie to specie. We can see the difference by analyzing the different protein models visually.
If all protein models have same function then all protein models are same?
Is it possible that all protein models are same for different species?
@@ahmedawan5909 There is this concept of HOMOLOGY. If there is one hundred percent amino acid sequence identity, then the proteins are identical. BUT many identical proteins have Isoforms due to PTM ( Post-Translational Modifications ) ,DIFFERENTIAL splicing and so on. Their identity will have to be evaluated on a case-by-case basis.
If you compare protein sequence across species, you will find sequences that are similar. They are not identical proteins ( strictly speaking). They are homologous proteins that perform the same function in a different species.
However, more distant species will have more variable sequences.
Agar secondary structure protein ka same ho teo tertiary structure bhe same hota hae KIA?
what is conf.score mean?
Its the Confidence Score. The higher the conf.score- the greater the confidence in the answer. For instance, in the case of I-Tasser's secondary structure prediction of protein, higher number/digit i.e 9 means that the predicted structure is dependable/reliable and if the number is close to zero than we can't really rely on such prediction. In other words it could be erroneous.
Good 🤩