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German Conference on Bioinformatics

GCB 1996: Bioinformatics pp 137–146Cite as

Fast protein fold recognition and accurate sequence-structure alignment

  • Molecular Modeling
  • Conference paper
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Part of the book series: Lecture Notes in Computer Science ((LNCS,volume 1278))

Abstract

We present two approaches to the sequence-structure alignment or threading problem: given an amino acid sequence and a protein structure, find the best mapping of sequence residues to structure positions with respect to some scoring system. Methods to solve this problem have two main applications: first, the recognition or identification of a plausible fold for a protein sequence of unknown structure out of a database of representative protein structures and, second, the computation of accurate alignments by improving on sequence alignments using structural information in order to find a better starting point for homology based modeling.

We describe the application of these threading methods to a blind prediction of the structure of thymidine kinase (TK) of herpes simplex virus I: in combination with standard alignment and alignment evaluation methods implemented in our software package ToPLign, we were able to identify a model structure and to build a quite accurate partial model of essential parts of the structure including the active site.

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Author information

Authors and Affiliations

  1. GMD - German National Research Center for Information Technology, SCAI - Institute for Algorithms and Scientific Computing, Schlo\ Birlinghoven, P.O. Box 1316, 53754, Sankt Augustin, Germany

    Ralf Zimmer & Ralf Thiele

Authors
  1. Ralf Zimmer
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  2. Ralf Thiele
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Editor information

Ralf Hofestädt Thomas Lengauer Markus Löffler Dietmar Schomburg

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© 1997 Springer-Verlag Berlin Heidelberg

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Zimmer, R., Thiele, R. (1997). Fast protein fold recognition and accurate sequence-structure alignment. In: Hofestädt, R., Lengauer, T., Löffler, M., Schomburg, D. (eds) Bioinformatics. GCB 1996. Lecture Notes in Computer Science, vol 1278. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0033212

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  • DOI: https://doi.org/10.1007/BFb0033212

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-63370-9

  • Online ISBN: 978-3-540-69524-0

  • eBook Packages: Springer Book Archive

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