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Explanation of input

PDB (Protein Data Bank) identifier is specified in a 4-character PDB assigned identifier. The chain identifier is defined by one-character as found in the PDB file for the desired chain. If the chain identifier is not provided, it will be assumed that this protein includes only one chain, with a blank chain identifier.
Users must input a PDB code which is present in PDB before Dec 08, 2006, otherwise, the user needs to upload a protein 3D structure file with PDB format.

If the query protein is a new structure or is not available in our PDB database, the user can upload a protein structure file with PDB format(*.ent or *.pdb) and input the chain identifier. If the chain identifier is not provided, it will be assumed that the uploaded file only includes one chain with a blank chain identifier. The upload structure file must be with minimum or at least HEADER and ATOM records in PDB format. The description of file format can be found in PDB guide webpage. Click here to download an example pdb file.

Explanation of output

"Length" is the alignment length of aligning a query structure to a subject structure by using BLAST with structural alphabets.

"Score" is the score of aligning a query structure to subject structure by using BLAST using structural alphabet substitution matrix (SASM). In general, more meaningful alignments correspond to lower E-values and higher scores.

"%_Iden" is the structural alphabet identity, which is similar to sequence identity in protein sequence alignment, of aligning a query structure to subject structure by using BLAST. It is given as (the number of identical alphabets)/ (alignment length).

"%_Gaps" is the gap percentage of aligning a query structure to a subject structure using BLAST with structural alphabets. It is given as (the number of gaps)/ (alignment length).

Do detailed structure alignment for structure visualisation/superimposition between query and subject structures.

This description is summarized from TITLE/HEADER in SCOP domain protein.