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 - 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 - 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 - GEN A1 - May, Patrick A1 - Bauer, Markus A1 - Köberle, Christian A1 - Klau, Gunnar T1 - A computational approach to microRNA detection N2 - 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. T3 - ZIB-Report - 06-44 KW - microRNA Smith-Waterman RNA folding Y1 - 2006 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-9383 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 - 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 - CHAP A1 - May, Patrick A1 - Klau, Gunnar A1 - Bauer, Markus A1 - Steinke, Thomas ED - Dubitzky, W. T1 - Accelerated microRNA-Precursor Detection Using the Smith-Waterman Algorithm on FPGAs T2 - GCCB Y1 - 2007 VL - 4360 SP - 19 EP - 32 PB - Springer 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 - 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 - 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 -