Automatic classification of protein structure by using Gauss integrals

Peter Røgen, B. Fain

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    We introduce a method of looking at, analyzing, and comparing protein structures. The topology of a protein is captured by 30 numbers inspired by Vassiliev knot invariants. To illustrate the simplicity and power of this topological approach, we construct a measure (scaled Gauss metric, SGM) of similarity of protein shapes. Under this metric, protein chains naturally separate into fold clusters. We use SGM to construct an automatic classification procedure for the CATH2.4 database. The method is very fast because it requires neither alignment of the chains nor any chain-chain comparison. It also has only one adjustable parameter. We assign 95.51% of the chains into the proper C (class), A (architecture), T (topology), and H (homologous superfamily) fold, find all new folds, and detect no false geometric positives. Using the SGM, we display a "map" of the space of folds projected onto two dimensions, show the relative locations of the major structural classes, and "zoom into" the space of proteins to show architecture, topology, and fold clusters. The existence of a simple measure of a protein fold computed from the chain path will have a major impact on automatic fold classification.
    Original languageEnglish
    JournalProceedings of the National Academy of Sciences of the United States of America
    Volume100
    Issue number1
    Pages (from-to)119-124
    ISSN0027-8424
    Publication statusPublished - 2003

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