TY - CHAP A1 - May, Patrick A1 - Krause, F. A1 - Ehrlich, C. A1 - Maaskola, J. A1 - Steinke, Thomas T1 - ZIB threading pipeline - A webservice-based, distributed structure prediction workflow. T2 - Proceedings of the German Conference on Bioinformatics (GCB) Y1 - 2005 SP - 125 EP - 126 ER - TY - CHAP A1 - May, Patrick A1 - Ehrlich, Hans-Christian A1 - Steinke, Thomas ED - Lehner, Wolfgang ED - Meyer, Norbert ED - Streit, Achim ED - Stewart, Craig T1 - ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services T2 - Euro-Par 2006 Workshops Y1 - 2006 UR - http://dx.doi.org/10.1007/11823285_121 VL - 4375 SP - 1148 EP - 1158 PB - Springer ER - TY - CHAP A1 - May, Patrick A1 - Steinke, Thomas A1 - Meyer, Michael T1 - THESEUS: A Parallel Threading Core T2 - Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow Y1 - 2004 SP - 199 ER - TY - CHAP A1 - May, Patrick A1 - Kallies, B. A1 - Steinke, Thomas T1 - THESEUS – a parallel threading core for highthroughput protein structure prediction T2 - Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC) Y1 - 2005 ER - TY - GEN A1 - May, Patrick A1 - Steinke, Thomas T1 - THESEUS - Protein Structure Prediction at ZIB N2 - 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. T3 - ZIB-Report - 06-24 KW - Protein Structure Prediction KW - Bioinformatics Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9184 ER - TY - JOUR A1 - May, Patrick A1 - Kreuchwig, A. A1 - Steinke, Thomas A1 - Koch, Ina T1 - PTGL: a database for secondary structure-based protein topologies JF - Nucleic Acids Res. Y1 - 2010 VL - 38 SP - D326 EP - 330 ER - TY - CHAP A1 - May, Patrick A1 - Koch, Ina ED - Christophe, C. ED - Lenhof, H.-P. ED - Sagot, M.-F. T1 - PTGL - Protein Topology Graph Library T2 - ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics Y1 - 2003 SP - 193 EP - 194 ER - TY - JOUR A1 - May, Patrick A1 - Barthel, Stefan A1 - Koch, Ina T1 - PTGL - a web-based database application for protein topologies JF - Bioinformatics Y1 - 2004 U6 - https://doi.org/10.1093/bioinformatics/bth367 VL - 20 IS - 17 SP - 3277 EP - 3279 ER - TY - CHAP A1 - Kolbeck, Björn A1 - Schmidt-Gönner, T. A1 - May, Patrick A1 - Knapp, E. T1 - Protein structure alignment based on contact maps and secondary structure. T2 - Proceedings of the German Conference on Bioinformatics (GCB) Y1 - 2005 SP - 122 EP - 123 ER - TY - JOUR A1 - Kolbeck, Björn A1 - May, Patrick A1 - Schmidt-Goenner, T. A1 - Steinke, Thomas A1 - Knapp, E. T1 - Connectivity independent protein-structure alignment: a hierarchical approach JF - BMC Bioinformatics Y1 - 2006 VL - 7 SP - 510 ER -