Data Entry

If you want some further information on how this method works, how to interpret the results and what prediction accuracies you can expect, please refer to the following paper:

Reinhardt and Eisenberg: "DPANN: Improved Sequence to Structure 
alignments Following Fold-Recognition" PROTEINS: Structure, Function and Genetics

Two inputs are needed for to perform the alignment:

1. The query sequence and its predicted secondary structure in pir-file format
2. The structure (or structures) and its (their) predicted secondary structure in pir-file format.

Please give the query in the following format:

>P1;Name
description if any
Sequence in one letter amino acid code, terminated by a "*"
>P1;SS
description if any
Predicted secondary structure in one letter code (H, E and C or "-"),  
terminated by a "*"

Please give the structure in the same format as described above. There can be more than one structure and its secondary structure given in the pir-formatted file, but each sequence always has to be folowed by its secondry structure directly.
Please also note that although you can use assigned secondary structure as well as predicted, the results of the alignment are going to be less reliable when mixing assigned and predicted secondary structure.