TY - JOUR
T1 - A computer vision based technique for 3-d sequence-independent structural comparison of proteins
AU - Bachar, Orly
AU - Fischer, Daniel
AU - Nussinov, Ruth
AU - Wolfson, Haim
N1 - Funding Information:
We would like to thank Drs R.Jernigan, D.Covell, J.Maizel and L.Young for discussions and suggestions. The research of R.Nussinov was sponsored by the National Cancer Institute, DHHS, under Contract No. l-CO-74102 with Program Resources, Inc. The contents of this publication do not necessarily reflect the views of policies of the DHHS, nor does mention of trade names, commercial products, or organizations imply endorsement by the US Government The research of HJ.Wolfson was supported in part by grant No. 83-00481 from the US-Israel Binational Science Foundation (BSF), Jerusalem, Israel. This work formed part of the PhD Thesis of D.Fischer, University of Tel Aviv.
PY - 1993/4
Y1 - 1993/4
N2 - 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.
AB - 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.
KW - 3-D protein motifs
KW - Computer vision
KW - Geometric hashing
KW - Protein folding
KW - Protein structural comparison
UR - http://www.scopus.com/inward/record.url?scp=0027238108&partnerID=8YFLogxK
U2 - 10.1093/protein/6.3.279
DO - 10.1093/protein/6.3.279
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AN - SCOPUS:0027238108
SN - 1741-0126
VL - 6
SP - 279
EP - 287
JO - Protein Engineering, Design and Selection
JF - Protein Engineering, Design and Selection
IS - 3
ER -