Protein structural alignment for detection of maximally conserved regions
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Updated: Aug 31, 2026

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Vladimir Kotlovyi1, William Lee Nichols, Lynn F Ten Eyck
1San Diego Supercomputer Center, University of California, San Diego 0505, 9500 Gilman Drive, La Jolla, CA 92093-0505, USA.
Abstract:
An algorithm for comparison of homologous protein structures and for study of conformational changes in proteins, has been developed. The method is based on identification of pieces of the two molecules that have similar shapes, as determined by the local conformation of the polypeptide chain. Pieces that superpose within a specified tolerance are assembled into domains based on similar transformations for superposition. The result is sets of pieces that represent conserved structural elements and conserved spatial relationships between structural elements within the proteins being compared. A similarity criterion based on maximum distance rather than on root mean square deviation reduces bias by outliers. The utility of the method is demonstrated by using examples from the protein kinase family.
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