About XML alignment format:

Since the residue-residue correspondence returned by ProMatch does not necessarily preserve the order of amino-acids in two proteins, the output of ProMatch is given in the form of an XML formatted alignment, as defined by Berbalk et al., 2009. Pairing of two residues in an XML formatted alignment is specified by a single <row> entry that contains two <meq> entries. An example alignment of Valine (V) in a first protein and Proline (P) in a second protein is given below.

<row><meq> 25 :V:A</meq><meq> 324 :P:A</meq></row>

As seen above, three fields are used to specify an amino acid. These fields are separated by a double colon (:) and correspond to pdb format ATOM records as follows:

The first field represents the residue sequence number followed by the insertion code (PDB columns 23-27).
The second field is the "residue type" (derived from three letter amino-acid code in columns 18-20).
The third field is the "chain identifier" (column 22).

More details about the XML alignment format can be found here.

We use <score> entry to specify the Z-score of a structure-structure alignment computed by ProMatch.


Berbalk,C., Schwaiger,C.S. and Lackner,P. (2009) Accuracy analysis of multiple structure alignments. Protein Sci., 18, 2027-2035.