Is there any software available to identify the central strands and end strands of a beta sheet or to identify the parallel and anti-parallel beta sheets?
I am not exactly sure what your question is but you could try BCL::Fold on 3D-structure predictions as well as with low resolution electron density data.
The software will use secondary structure prediction to generate a pool of ensembles that are placed into site. When the pool is empty there will be a score and another try.
One of the scoring criteria is the end to end distance, like, can the remaining residues form a loop in between the two structures?
This way you get a very good guess if your beta sheets are parallel or anti-parallel and also an initial model.
S.
@Stefan......My main aim is to find the type of beta strand. Suppose I run STRIDE and now I want to find the strands making a sheet. Among those strand which one is in the middle and which one are in the end. For example 1-2-3 strands make a sheet so 2 is in the middle and 1,3 in the end.........so how to find that..... I have 3D coordinates..........
Neway I will try BCL::Fold......... I never heard of it.........thanx alot for the response
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