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Max. sequence offset

Sequence offset is used to obtain sequence dependent comparisons. One assumes that a direct 1:1 correspondence between the protein sequences exists, and only residues aligned with offset not greater than k will be counted. This mode is especially useful for comparing models of the same protein in structure prediction applications. If lengths of compared structures differ, offset is measured from the closest alignment with gaps located only in the shorter sequence.

Max. sequence swaps

Maximal number of segment swaps allowed in the computed alignment. -1 denotes infinity. During computation, if the processed alignment contains more swaps than the given limit, the largest subalignment containing the maximal number of swaps will be considered. E.g. value 1 means that only circular permutations and alignments without swaps will be returned.

Structure

PDB or SCOP code

Code of a protein structure in PDB or SCOP databases. PDB codes are composed of 4 alphanumerical characters (e.g. 1m55), and can be followed by a letter denoting a chosen chain (e.g. 1m55A) (otherwise the whole molecule will be used in an alignment). Codes of SCOP domains are 7 characters long, and begin with letter d (e.g. d1m55a_).

File

A properly formatted all atom PDB file should be uploaded. Coordinates of sidechain atoms are required to determine geometrical centers of residues which are used to compute inter-residue contacts. Structures having fewer than 5 residues are considered invalid. Multiple chains are accepted although submitting entire crystal cells with internal symmetries may significantly increase the computation time providing multiple insignificant alignments.