Simloc: detection of local similarities

(M. Mezei, Prot. Engng., 7, 331-333 (1994))

Last updated: 10/06/03

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Simloc compares two conformation of a molecule and, by comparing the local environments of each bond, detects the one that are candidate for hinges. Once hinges have been identified (depending on a threshold parameter) the hinge bonds are deleted and the resulting fragments are superimposed to see if the RMS has decreased.

The program allows the user to vary the threshold parameter and obtain smaller or larger fragments.

In the example below, two conformations of the backbone of the protein Calmodulin are superimposed showing fairly large deviations. The smaller picture displays a segment found by Simloc that shows significantly closer similarity.

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