BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
| العنوان: | BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry |
|---|---|
| المؤلفون: | Modesto Orozco, Manuel Rueda, Ruben Abagyan, Maxim Totrov |
| المساهمون: | Universitat de Barcelona |
| المصدر: | Recercat. Dipósit de la Recerca de Catalunya instname BMC Structural Biology Rueda, Manuel; Orozco, Modesto; Totrov, Maxim; & Abagyan, Ruben. (2013). BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry. BMC Structural Biology, 13(1), 32. doi: http://dx.doi.org/10.1186/1472-6807-13-32Test. Retrieved from: http://www.escholarship.org/uc/item/9dh1d8z8Test Dipòsit Digital de la UB Universidad de Barcelona |
| بيانات النشر: | BioMed Central |
| مصطلحات موضوعية: | Models, Molecular, Web server, Computer science, Protein Conformation, Rotational symmetry, computer.software_genre, Protein Structure, Secondary, Biologia computacional, Computational biology, 03 medical and health sciences, User-Computer Interface, Biomolècules, Structural Biology, Computer Graphics, Superimposition, Databases, Protein, Interactive visualization, Root-mean-square deviation, 030304 developmental biology, Oligòmers, Biomolecules, 0303 health sciences, Internet, 030302 biochemistry & molecular biology, Computational Biology, Proteins, computer.file_format, Protein Data Bank, Protein Structure, Tertiary, Crystallography, Oligomers, Symmetry (geometry), Protein Multimerization, computer, Algorithm, Proteïnes, Software, Generator (mathematics) |
| الوصف: | Background Most of the proteins in the Protein Data Bank (PDB) are oligomeric complexes consisting of two or more subunits that associate by rotational or helical symmetries. Despite the myriad of superimposition tools in the literature, we could not find any able to account for rotational symmetry and display the graphical results in the web browser. Results BioSuper is a free web server that superimposes and calculates the root mean square deviation (RMSD) of protein complexes displaying rotational symmetry. To the best of our knowledge, BioSuper is the first tool of its kind that provides immediate interactive visualization of the graphical results in the browser, biomolecule generator capabilities, different levels of atom selection, sequence-dependent and structure-based superimposition types, and is the only web tool that takes into account the equivalence of atoms in side chains displaying symmetry ambiguity. BioSuper uses ICM program functionality as a core for the superimpositions and displays the results as text, HTML tables and 3D interactive molecular objects that can be visualized in the browser or in Android and iOS platforms with a free plugin. Conclusions BioSuper is a fast and functional tool that allows for pairwise superimposition of proteins and assemblies displaying rotational symmetry. The web server was created after our own frustration when attempting to superimpose flexible oligomers. We strongly believe that its user-friendly and functional design will be of great interest for structural and computational biologists who need to superimpose oligomeric proteins (or any protein). BioSuper web server is freely available to all users at http://ablab.ucsd.edu/BioSuperTest. |
| وصف الملف: | application/pdf |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a603f8e201e9c75a59fbd2abc5fc274bTest http://hdl.handle.net/2445/54510Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....a603f8e201e9c75a59fbd2abc5fc274b |
| قاعدة البيانات: | OpenAIRE |
| الوصف غير متاح. |