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THESEUS - Protein Structure Prediction at ZIB

Please always quote using this URN: urn:nbn:de:0297-zib-9184
  • THESEUS, the ZIB threading environment, is a parallel implementation of a protein threading based on a multi-queued branch-and-bound optimal search algorithm to find the best sequence-to-structure alignment through a library of template structures. THESEUS uses a template core model based on secondary structure definition and a scoring function based on knowledge-based potentials reflecting pairwise interactions and the chemical environment, as well as pseudo energies for homology detection, loop alignment, and secondary structure matching. The threading core is implemented in C++ as a SPMD parallization architecture using MPI for communication. The environment is designed for generic testing of different scoring functions, e.g. different secondary structure prediction terms, different scoring matrices and information derived from multiple sequence alignments. A validaton of the structure prediction results has been done on the basis of standard threading benchmark sets. THESEUS successfully participated in the 6th Critical Assessment of Techniques for Protein Structure Prediction (CASP) 2004.

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Author:Patrick May, Thomas Steinke
Document Type:ZIB-Report
Tag:Bioinformatics; Protein Structure Prediction
MSC-Classification:92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92-08 Computational methods
92-XX BIOLOGY AND OTHER NATURAL SCIENCES / 92Exx Chemistry (For biochemistry, see 92C40) / 92E10 Molecular structure (graph-theoretic methods, methods of differential topology, etc.)
Date of first Publication:2006/05/18
Series (Serial Number):ZIB-Report (06-24)
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