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Updated: Aug 26, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
ParSeq: searching motifs with structural and biochemical properties
M Schmollinger1, I Fischer, C Nerz
1Center for Bioinformatics, University of Tubingen, Sand 14, 72076 Tubingen, Germany.
Summary:
Searches for variable motifs such as protein-binding sites or promoter regions are more complex than the search for casual motifs. For example, in amino acid sequences comparing motifs alone mostly proves to be insufficient to detect regions that represent proteins with a special function, because the function depends on biochemical properties of individual amino acids (such as polarity or hydrophobicity). Pure string matching programs are not able to find these motifs; hence, we developed ParSeq, a program that combines the search for motifs with certain structural properties, the verification of biochemical properties, an approximate search mechanism and a stepwise creation of the motif description by allowing to search on previously obtained results.
Availability:
http://www-pr.informatik.uni-tuebingen.de/parseq
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