[Radel]

Hello,

I'm looking in some databases' sites for sequences of proteins, with its secondary structure well-known (no predicted by computer algorithm, that its based on some probabilistic stuff).

I found some popular sites, but im not able to find, for example in PDS site, the structure displayed like that:
Amino acid position 1 -------------- Helix.
Amino acid position 2---------------Helix.
Amino acid position 3---------------Beta.

etc.

Where can I find well-known protein secondary structures with its amino acid sequence?

Thank you for your time, and sorry for newbie question.

[Babcock_Hall]

http://pdbwiki.org/wiki/PDB_FAQ#Defining_Secondary_Structure_Elements_in_structures
What is PDS?
I was surprised to read this about the protein data bank (PDB) files:
"The PDB files in the RCSB contain information about the secondary structure of protein entries. This information is called the 'authors definition'. You should be careful if you use the secondary structure assignments provided by the authors in the PDB file. You might expect that they are of high quality because they were curated by people who know the proteins quite well. But I there are frequently overlaps between different secondary structure elements. Also, not all PDB entries contain secondary structure assignments.
You can assign secondary structures using a several different automatic methods:"

[Radel]

Hello and thanks for your reply.

I ask for this because I am trying to make an algorithm to predict secondary structure of proteins. I am not a chemist, but a computer science begginer. I have already studied "gor" algorithm that calculates with a good accuracy the 2 structure.
For my algorithm, I need to know the well-known relation between amino acid and the kind of structure such:

Amino acid position 1 -------------- Helix.
Amino acid position 2---------------Helix.
Amino acid position 3---------------Beta.

In order to check if my algorithm is doing its work correctly.

[aHerraez]

One (if not the most) established method for assigment of secondary structure is DSSP, by Kabsch and Sander
I would not expect that your efforts will be too worthy. That is an old field.