when we do superpose of 3 pdbs together (1 on 2, 2 on 3, 3 on 1) and after that if we change the sequence of superposition, will there be any possibility to see the change in RMSD value (before and after)
@Thanks Elvis,
yes they are of same protein but are different X-ray crystal submitted by different groups. Even some possess outliers and also different resolution, would this be not the reason of getting different RMSD values, when protein superpose sequence get changed?
If you want superpose more than 2 pdbs in a way that your results are less dependent from the sequence of the paired superpositions a good strategy is to define a common core of residues between all of them and then use this core for superpose all the models. If the core of the superposition varies each time you perform a superposition (e.g.. when 1 on 2 the core is different from 2 on 3) then obviously the results will be different if you will perform in a different order.
Thanks @ elvis and massimo, they are the same protein with crystal struture.now what i could conclude is that if i superpose same protein of various resolution, everytime i change the sequencr of superpose, will get different rmsd like 1 over 2 and 2 over 1 (rmsd 0.98 and 0.76). Is there any paper regarding this?
The main question you have to answer is the method that have been used to determine the spatial locations of the atoms within the proteins that you compare!
Sincerely
CC
I would recommend to define the conserved regular secondary elements of the three proteins, and duperpose on this core of conserved elements (only the backbone atoms)
Hope this helps
Hi Arvind. How do you superpose 1 to 2 and 2 to 1? What kind of algorithm or program are you using? Again if you superpose 1 to 2 and the core determined automatically is different from the core computed when you superpose 2 and 1 you will end up with different rmsd. You will obtain the same rmsd only if you match always the same atoms, that is if you are considering the same core. The fact that changing the sequence of superposition programs can select a different core is because secondary structure matching are not deterministic algorithm but there is a component that depends from where you are starting from. When you superpose do not just look only to the RMSD but also to the aligned core of residues employed it is extremely important: it is not the same a rmsd 0.5 A computed over 130 residues of 130 residues than a rmsd of 0.5 A computer over 10 residues of 130.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics