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- Title
Moment invariants as shape recognition technique for comparing protein binding sites.
- Authors
Ingolf Sommer; Oliver Müller; Francisco S. Domingues; Oliver Sander; Joachim Weickert; Thomas Lengauer
- Abstract
Motivation: An approach for identifying similarities of protein–protein binding sites is presented. The geometric shape of a binding site is described by computing a feature vector based on moment invariants. In order to search for similarities, feature vectors of binding sites are compared. Similar feature vectors indicate binding sites with similar shapes. Results: The approach is validated on a representative set of protein–protein binding sites, extracted from the SCOPPI database. When querying binding sites from a representative set, we search for known similarities among 2819 binding sites. A median area under the ROC curve of 0.98 is observed. For half of the queries, a similar binding site is identified among the first two of 2819 when sorting all binding sites according the proposed similarity measure. Typical examples identified by this method are analyzed and discussed. The nitrogenase iron protein-like SCOP family is clustered hierarchically according to the proposed similarity measure as a case study. Availability: Python code is available on request from the authors. Contact: sommer@mpi-inf.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.
- Publication
Bioinformatics, 2007, Vol 23, Issue 23, p3139
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btm503