BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry

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...

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Autores: Rueda Borrego, Manuel, Orozco López, Modesto, Totrov, Maxim, Abagyan, Ruben
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2013
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/54510
Acceso en línea:https://hdl.handle.net/2445/54510
Access Level:acceso abierto
Palabra clave:Proteïnes
Biomolècules
Biologia computacional
Oligòmers
Proteins
Biomolecules
Computational biology
Oligomers
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spelling BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetryRueda Borrego, ManuelOrozco López, ModestoTotrov, MaximAbagyan, RubenProteïnesBiomolèculesBiologia computacionalOligòmersProteinsBiomoleculesComputational biologyOligomersBackground 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/BioSuper webcite.BioMed Central2013info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/54510Articles publicats en revistes (Bioquímica i Biomedicina Molecular)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: http://doi.dx.org.10.1186/1472-6807-13-32BMC Structural Biology, 2014, vol. 13, num. 32, p. 1-9http://dx.doi.org/10.1186/1472-6807-13-32info:eu-repo/grantAgreement/EC/FP7/291433cc-by (c) Rueda Borrego, Manuel et al., 2014http://creativecommons.org/licenses/by/3.0/esinfo:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/545102026-05-27T06:46:51Z
dc.title.none.fl_str_mv BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
title BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
spellingShingle BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
Rueda Borrego, Manuel
Proteïnes
Biomolècules
Biologia computacional
Oligòmers
Proteins
Biomolecules
Computational biology
Oligomers
title_short BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
title_full BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
title_fullStr BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
title_full_unstemmed BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
title_sort BioSuper: A web tool for the superimposition of biomolecules and assemblies with rotational symmetry
dc.creator.none.fl_str_mv Rueda Borrego, Manuel
Orozco López, Modesto
Totrov, Maxim
Abagyan, Ruben
author Rueda Borrego, Manuel
author_facet Rueda Borrego, Manuel
Orozco López, Modesto
Totrov, Maxim
Abagyan, Ruben
author_role author
author2 Orozco López, Modesto
Totrov, Maxim
Abagyan, Ruben
author2_role author
author
author
dc.subject.none.fl_str_mv Proteïnes
Biomolècules
Biologia computacional
Oligòmers
Proteins
Biomolecules
Computational biology
Oligomers
topic Proteïnes
Biomolècules
Biologia computacional
Oligòmers
Proteins
Biomolecules
Computational biology
Oligomers
description 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/BioSuper webcite.
publishDate 2013
dc.date.none.fl_str_mv 2013
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/54510
url https://hdl.handle.net/2445/54510
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: http://doi.dx.org.10.1186/1472-6807-13-32
BMC Structural Biology, 2014, vol. 13, num. 32, p. 1-9
http://dx.doi.org/10.1186/1472-6807-13-32
info:eu-repo/grantAgreement/EC/FP7/291433
dc.rights.none.fl_str_mv cc-by (c) Rueda Borrego, Manuel et al., 2014
http://creativecommons.org/licenses/by/3.0/es
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Rueda Borrego, Manuel et al., 2014
http://creativecommons.org/licenses/by/3.0/es
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv Articles publicats en revistes (Bioquímica i Biomedicina Molecular)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,301603

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