Fast protein fold recognition and accurate sequence-structure alignment

  • Ralf Zimmer
  • Ralf Thiele
Molecular Modeling
Part of the Lecture Notes in Computer Science book series (LNCS, volume 1278)


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.


Herpes Simplex Virus Type Alignment Method Adenylate Kinase Fold Recognition Pair Interaction Potential 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 1997

Authors and Affiliations

  • Ralf Zimmer
    • 1
  • Ralf Thiele
    • 1
  1. 1.GMD - German National Research Center for Information TechnologySCAI - Institute for Algorithms and Scientific ComputingSankt AugustinGermany

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