Aleksandra I Jarmolinska1,2, Michal Kadlof1,3, Pawel Dabrowski-Tumanski1,4, Joanna I Sulkowska1,4. 1. Centre of New Technologies, University of Warsaw, Warsaw, Poland. 2. College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, Warsaw, Poland. 3. Faculty of Physics, University of Warsaw, Warsaw, Poland. 4. Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
Abstract
Motivation: Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos and links). As the topology is fundamental for the proper function of proteins, modeling of topologically correct structures is decisive in various fields, including biophysics, biotechnology and molecular biology. However, none of the currently existing tools take into account the topology of the model and those which could be modified to include topology, demand experience in bioinformatics, protein topology and knot theory. Results: In this work, we present the GapRepairer-the server that fills the gap in the spectrum of structure modeling methods. Its easy and intuitive interface offers the power of Modeller homology modeling to many non-experts in the field. This server determines the topology of templates and predicted structures. Such information when possible is used by the server to suggest the best model, or it can be used by the user to score models or to design artificially (dis)entangled structures. Availability and implementation: GapRepairer server along with tutorials, usage notes, movies and the database of already repaired structures is available at http://gaprepairer.cent.uw.edu.pl. Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation: Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos and links). As the topology is fundamental for the proper function of proteins, modeling of topologically correct structures is decisive in various fields, including biophysics, biotechnology and molecular biology. However, none of the currently existing tools take into account the topology of the model and those which could be modified to include topology, demand experience in bioinformatics, protein topology and knot theory. Results: In this work, we present the GapRepairer-the server that fills the gap in the spectrum of structure modeling methods. Its easy and intuitive interface offers the power of Modeller homology modeling to many non-experts in the field. This server determines the topology of templates and predicted structures. Such information when possible is used by the server to suggest the best model, or it can be used by the user to score models or to design artificially (dis)entangled structures. Availability and implementation: GapRepairer server along with tutorials, usage notes, movies and the database of already repaired structures is available at http://gaprepairer.cent.uw.edu.pl. Supplementary information: Supplementary data are available at Bioinformatics online.