@misc{MaySteinke, author = {May, Patrick and Steinke, Thomas}, title = {THESEUS - Protein Structure Prediction at ZIB}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9184}, number = {06-24}, abstract = {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.}, language = {en} } @article{MayKreuchwigSteinkeetal.2010, author = {May, Patrick and Kreuchwig, A. and Steinke, Thomas and Koch, Ina}, title = {PTGL: a database for secondary structure-based protein topologies}, series = {Nucleic Acids Res.}, volume = {38}, journal = {Nucleic Acids Res.}, pages = {D326 -- 330}, year = {2010}, language = {en} } @inproceedings{KolbeckSchmidtGoennerMayetal.2005, author = {Kolbeck, Bj{\"o}rn and Schmidt-G{\"o}nner, T. and May, Patrick and Knapp, E.}, title = {Protein structure alignment based on contact maps and secondary structure.}, series = {Proceedings of the German Conference on Bioinformatics (GCB)}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB)}, pages = {122 -- 123}, year = {2005}, language = {en} } @inproceedings{MayKalliesSteinke2005, author = {May, Patrick and Kallies, B. and Steinke, Thomas}, title = {THESEUS - a parallel threading core for highthroughput protein structure prediction}, series = {Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC)}, booktitle = {Proceedings of the 7th Congress of the World Association of Theoretically Orientes Chemists (WARTOC)}, year = {2005}, language = {en} } @inproceedings{MayKrauseEhrlichetal.2005, author = {May, Patrick and Krause, F. and Ehrlich, C. and Maaskola, J. and Steinke, Thomas}, title = {ZIB threading pipeline - A webservice-based, distributed structure prediction workflow.}, series = {Proceedings of the German Conference on Bioinformatics (GCB)}, booktitle = {Proceedings of the German Conference on Bioinformatics (GCB)}, pages = {125 -- 126}, year = {2005}, language = {en} } @inproceedings{MichalskyGoedePreissneretal.2004, author = {Michalsky, E. and Goede, A. and Preissner, Robert and May, Patrick and Steinke, Thomas}, title = {A distributed pipeline for structure prediction}, series = {CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy}, booktitle = {CASP6 Abstract Book, Sixth Meeting on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy}, pages = {112 -- 114}, year = {2004}, language = {en} } @article{MayBarthelKoch2004, author = {May, Patrick and Barthel, Stefan and Koch, Ina}, title = {PTGL - a web-based database application for protein topologies}, series = {Bioinformatics}, volume = {20}, journal = {Bioinformatics}, number = {17}, doi = {10.1093/bioinformatics/bth367}, pages = {3277 -- 3279}, year = {2004}, language = {en} } @inproceedings{MaySteinkeMeyer2004, author = {May, Patrick and Steinke, Thomas and Meyer, Michael}, title = {THESEUS: A Parallel Threading Core}, series = {Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow}, booktitle = {Procs. 12th Internat. Conf. on Intelligent Systems for Mol. Bio. (ISMB) and 3rd European Conf. on Comp. Bio. (ECCB), Glasgow}, pages = {199}, year = {2004}, language = {en} } @inproceedings{MayEhrlichSteinke2006, author = {May, Patrick and Ehrlich, Hans-Christian and Steinke, Thomas}, title = {ZIB Structure Prediction Pipeline: Composing a Complex Biological Workflow Through Web Services}, series = {Euro-Par 2006 Workshops}, volume = {4375}, booktitle = {Euro-Par 2006 Workshops}, editor = {Lehner, Wolfgang and Meyer, Norbert and Streit, Achim and Stewart, Craig}, publisher = {Springer}, pages = {1148 -- 1158}, year = {2006}, language = {en} } @article{KolbeckMaySchmidtGoenneretal.2006, author = {Kolbeck, Bj{\"o}rn and May, Patrick and Schmidt-Goenner, T. and Steinke, Thomas and Knapp, E.}, title = {Connectivity independent protein-structure alignment: a hierarchical approach}, series = {BMC Bioinformatics}, volume = {7}, journal = {BMC Bioinformatics}, pages = {510}, year = {2006}, language = {en} } @inproceedings{RotherTrisslMuelleretal.2003, author = {Rother, Kristian and Trissl, S. and M{\"u}ller, H. and May, Patrick and Heek, R. and Preissner, Robert and Steinke, Thomas and Koch, Ina and Leser, Ulf and Fr{\"o}mmel, Cornelius}, title = {Columba - A Database of Annotations of Protein Structure}, series = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, booktitle = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, editor = {Christophe, C. and Lenhof, H.-P. and Sagot, M.-F.}, pages = {109 -- 110}, year = {2003}, language = {en} } @inproceedings{MayKlauBaueretal.2007, author = {May, Patrick and Klau, Gunnar and Bauer, Markus and Steinke, Thomas}, title = {Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs}, series = {GCCB}, volume = {4360}, booktitle = {GCCB}, editor = {Dubitzky, W.}, publisher = {Springer}, pages = {19 -- 32}, year = {2007}, language = {en} } @inproceedings{MayKoch2003, author = {May, Patrick and Koch, Ina}, title = {PTGL - Protein Topology Graph Library}, series = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, booktitle = {ECCB - Proceedings of the European Conference on Computational Biology in conjunction with the French National Conference on Bioinformatics}, editor = {Christophe, C. and Lenhof, H.-P. and Sagot, M.-F.}, pages = {193 -- 194}, year = {2003}, language = {en} } @misc{MayBauerKoeberleetal., author = {May, Patrick and Bauer, Markus and K{\"o}berle, Christian and Klau, Gunnar}, title = {A computational approach to microRNA detection}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-9383}, number = {06-44}, abstract = {During the last few years more and more functionalities of RNA have been discovered that were previously thought of being carried out by proteins alone. One of the most striking discoveries was the de tection of microRNAs, a class of noncoding RNAs that play an important role in post-transcriptional gene regulation. Large-scale analyses are needed for the still increasingly growing amount of sequen ce data derived from new experimental technologies. In this paper we present a framework for the detection of the distinctive precursor structure of microRNAS that is based on the well-known Smith-Wat erman algorithm and various filtering steps. We conducted experiments on real genomic data and we found several new putative hits for microRNA precursor structures.}, language = {en} }