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Brunnert, Marcus
Fischer, Paul
Urfer, Wolfgang
Year of Publication: 
Series/Report no.: 
Technical Report 2002,61
The expanding availability of protein data enforces the application of empirical methods necessary to recognize protein structures. In this paper a sequence-structure alignment method is described and applied to various Ubiquitin-like folded Ras-binding domains. On the basis of two probability functions that evaluate similarities between the occurrence of amino-acids in the primary and secondary protein structure, different versions of simple scoring functions are proposed. The application of the program ’PLACER’ that uses a dynamic programming approach enables the search for an optimal sequence-structure alignment and the prediction of the secondary structure.
Sequence-structure alignment
core model
dynamic programming
secondary structure prediction
Document Type: 
Working Paper

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