All-to-All Protein Structure Alignment by CE Results - Help
Topics are arranged alphabetically
ID
Polypeptide chain ID is represented in the form: PPPP:C
where PPPP is the 4-character PDB assigned entry identifier and C
is the chain identifier as found in the PDB file for the desired chain.
An underscore (_) is used to indicate chains with blank
chain identifier in corresponding PDB file.
User input files are assigned the PDB identifier USR1 [and USR2].
Z-Score
Measure of the statistical significance of the result relative to an alignment
of random structures.
RMSD (Root Mean Square Deviation)
RMSD is evaluated based on C alpha atoms over the length
of the alignment.
Members of the same protein family which obviously have the same fold can
differ by up to 4 Angstroms or more in RMSD. Useful results may be in the
twighlight zone of greater than 4 Angstroms.
Seq. (Sequence Identity)
Percentage of amino-acid identities in alignment relative to all positions
in alignment. Identity below 30% has a good chance of random occurence,
especially for shorter alignments.
Aligned/Size (Number of Positions)
Number of aligned position and total number of residues for a given protein
in the table.
Gap (Number of Gaps)
Number of positions
that have no recognized partner in the other protein being aligned. Number of aligned position and total number of residues for a given protein
in the table.
Exp. (Experimental Method)
Exprerimental procedure used in structure determination.
Name
Chain name as described by first 80 characters of COMPND record in PDB file.