A computer vision based technique for 3-d sequence-independent structural comparison of proteins

Orly Bachar, Daniel Fischer, Ruth Nussinov*, Haim Wolfson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


A detailed description of an efficient approach to comparison of protein structures is presented. Given the 3-D coordinate data of the structures to be compared, the system automatically identifies every region of structural similarity between the structures without prior knowledge of an initial alignment. The method uses the geometric hashing technique which was originally developed for model-based object recognition problems in the area of computer vision. It exploits a rotationally and translationally invariant representation of rigid objects, resulting in a highly efficient, fully automated tool. The method is independent of the amino acid sequence and, thus, insensitive to insertions, deletions and displacements of equivalent substructures between the molecules being compared. The method described here is general, identifies 'real' 3-D substructures and is not constrained by the order imposed by the primary chain of the amino adds. Typical structure comparison problems are examined and the results of the new method are compared with the published results from previous methods. These results, obtained without using the sequence order of the chains, confirm published structural analogies that use sequence-dependent techniques. Our results also extend previous analogies by detecting geometrically equivalent out of- sequential-order structural elements which cannot be obtained by current techniques.

Original languageEnglish
Pages (from-to)279-287
Number of pages9
JournalProtein Engineering, Design and Selection
Issue number3
StatePublished - Apr 1993


FundersFunder number
US-Israel Binational Science Foundation
National Institutes of HealthN01CO074102
National Cancer Institute
Department of Health and Human Services, State Government of Victoria83-00481
United States-Israel Binational Science Foundation


    • 3-D protein motifs
    • Computer vision
    • Geometric hashing
    • Protein folding
    • Protein structural comparison


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