ss_struct-big.png We employ the method STRIDE to derive the secondary structure assignment from co-ordinates.

The types of secondary structure that are highlighted are:

Unfortunately, STRIDE does not know anything about modified residues, though PDB files have a MODRES that indicate the nature of the modification and the original standard residue name. Therefore, some amino acids do not have an assigned secondary structure.

Reference

Frishman, D. and Argos, P. (1995) Knowledge-based protein secondary structure assignment. Proteins, 23, 566-579.

DirectAccessURL

URL for direct computation of results of this tool:

http://i.moltalk.org/secondary_structure/3/PDB/1QMZ/65

parameters:

toolchain
"secondary_structure"
position
"3"
strx source
"PDB" or "model"
strx id
4-letter pdb code or unique identifier of uploaded model
chaincode
ASCII value of chain identifier (A=65, B=66, ' '=32, ...)