Questions tagged [secondary-structure]

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which secondary structure assignment algorithm is used by PDB?

older releases of PDB used to specify DSSP as the 2ary structure assignment algorithm used in PDB, right now no algorithm is explicitly stated. Where can I find a reference for it in the database?
raysas's user avatar
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Is there any python module to assign secondary structures which includes both Polyprolene region as well as individual strand as well?

I wanted to assign secondary structure to set of pdb files. However, DSSP and STRIDE cannot assign for single peptides if it is falling inside single long beta strand or polyprolene region as it does ...
vigneshwaran kannan's user avatar
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Program for SOV calculation

Are there any programs (web server or installable) out there to calculate segment overlap score (SOV) for protein secondary structures? Thanks
Balint Biro's user avatar
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Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
Aalawlx's user avatar
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Is there a software that extract molecular descriptors of single stranded RNAs secondary structure from dot bracket notation in nucleotide resolution?

I want to generate descriptors from dot bracket notations of single stranded RNA/DNA secondary structures. So far i have come across this paper:
Gojih's user avatar
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