SURF’s UP! — Protein classification by surface comparisons View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2007-01

AUTHORS

Joanna M Sasin, Adam Godzik, Janusz M Bujnicki

ABSTRACT

Large-scale genome sequencing and structural genomics projects generate numerous sequences and structures for 'hypothetical' proteins without functional characterizations. Detection of homology to experimentally characterized proteins can provide functional clues, but the accuracy of homology-based predictions is limited by the paucity of tools for quantitative comparison of diverging residues responsible for the functional divergence. SURF'S UP! is a web server for analysis of functional relationships in protein families, as inferred from protein surface maps comparison according to the algorithm. It assigns a numerical score to the similarity between patterns of physicochemical features(charge, hydrophobicity) on compared protein surfaces. It allows recognizing clusters of proteins that have similar surfaces, hence presumably similar functions. The server takes as an input a set of protein coordinates and returns files with "spherical coordinates" of proteins in a PDB format and their graphical presentation, a matrix with values of mutual similarities between the surfaces, and the unrooted tree that represents the clustering of similar surfaces, calculated by the neighbor-joining method. SURF'S UP! facilitates the comparative analysis of physicochemical features of the surface, which are the key determinants of the protein function. By concentrating on coarse surface features, SURF'S UP! can work with models obtained from comparative modelling. Although it is designed to analyse the conservation among homologs, it can also be used to compare surfaces of non-homologous proteins with different three-dimensional folds, as long as a functionally meaningful structural superposition is supplied by the user. Another valuable characteristic of our method is the lack of initial assumptions about the functional features to be compared. SURF'S UP! is freely available for academic researchers at http://asia.genesilico.pl/surfs_up/. More... »

PAGES

97-100

References to SciGraph publications

  • 2003-12. Automatic prediction of protein function in CELLULAR AND MOLECULAR LIFE SCIENCES
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s12038-007-0009-0

    DOI

    http://dx.doi.org/10.1007/s12038-007-0009-0

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/17426383


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