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Geometrical core

Geometrical core

  

Alignment (example):

Distance spreading (Å)
 Minimal core size
 Bron – Kerbosh algorithm timeout (secs)
Alternative core new atoms (%)
 Cores count (0 for all)
 Superposition core identifier (0 for the main core)

Definitions

Alignment

An alignment of a set of structures is a set of positions, to each position some atoms from different structures correspond. In this service, only CA-atoms are included into alignments.

In a text representation of an alignment, all CA-atoms of the residues that are at the same position in different sequences form a position of the alignment (i.e., the first letters of the sequences form one position, the second ones — another position, etc.).

Geometrical core

Geometrical core of a set of structures is a subset of alignment positions those atoms are disposed similarly in all structures.

Difference of distance between corresponding atoms is used as the measure of similarity of the disposition.

For any two positions included into geometrical core, the distances between CA atoms of those positions in all structures may differ not more than the value of the parameter "Distance spreading".

Alternative cores

One alignment can produce more than one geometrical core. The largest of them is called the "main core". Different cores can include some common atoms.

Algorithm: Sergei Spirin, Andrei Alexeevski, Boris Nagaev
Programming: Boris Nagaev (computation), Sergei Spirin (web-interface)
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