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CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.ORCID-id: 0000-0001-8303-4481
2016 (engelsk)Inngår i: Journal of Computational Chemistry, ISSN 0192-8651, E-ISSN 1096-987X, Vol. 37, nr 22, s. 2098-2105Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

CarbBuilder is a portable software tool for producing three-dimensional molecular models of carbohydrates from the simple text specification of a primary structure. CarbBuilder can generate a wide variety of carbohydrate structures, ranging from monosaccharides to large, branched polysaccharides. Version 2.0 of the software, described in this article, supports monosaccharides of both mammalian and bacterial origin and a range of substituents for derivatization of individual sugar residues. This improved version has a sophisticated building algorithm to explore the range of possible conformations for a specified carbohydrate molecule. Illustrative examples of models of complex polysaccharides produced by CarbBuilder demonstrate the capabilities of the software. CarbBuilder is freely available under the Artistic License 2.0.

sted, utgiver, år, opplag, sider
2016. Vol. 37, nr 22, s. 2098-2105
Emneord [en]
carbohydrate, polysaccharide conformation, C, Albicans, 3D model, Shigella flexneri
HSV kategori
Forskningsprogram
organisk kemi
Identifikatorer
URN: urn:nbn:se:su:diva-133371DOI: 10.1002/jcc.24428ISI: 000379941300007PubMedID: 27317625OAI: oai:DiVA.org:su-133371DiVA, id: diva2:968071
Forskningsfinansiär
Swedish Research CouncilTilgjengelig fra: 2016-09-12 Laget: 2016-09-06 Sist oppdatert: 2018-10-18bibliografisk kontrollert
Inngår i avhandling
1. Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics
Åpne denne publikasjonen i ny fane eller vindu >>Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics
2017 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
Abstract [en]

Carbohydrates are ubiquitous components in nature involved in a range of tasks. They cover every cell and contribute both structural stability as well as identity. Lipopolysaccharides are the outermost exposed part of the bacterial cell wall and the primary target for host-pathogen recognition. Understanding the structure and biosynthesis of these polysaccharides is crucial to combat disease and develop new medicine. Structural determinations can be carried out using NMR spectroscopy, a powerful tool giving information on an atomistic scale. This thesis is focused on method development to study polysaccharide structures as well as application on bacterial lipopolysaccharides. The focus has been to incorporate a bioinformatics approach prior to analysis by NMR spectroscopy, and then computer assisted methods to aid in the subsequent analysis of the spectra.

The third chapter deals with the recent developments of ECODAB, a tool that can help predict structural fragments in Escherichia coli O-antigens. It was migrated to a relational database and the aforementioned predictions can now be made automatically by ECODAB. The fourth chapter gives insight into the program CASPER, a computer program that helps with structure determination of oligo- and polysaccharides. An approach to determine substituent positions in polysaccharides was investigated. The underlying database was also expanded and the improved capabilities were demonstrated by determining O-antigenic structures that could not previously be solved. The fifth chapter is an application to O‑antigen structures of E. coli strains. This is done by a combination of NMR spectroscopy and bioinformatics to predict components as well as linkages prior to spectra analysis. In the first case, a full structure elucidation was performed on E. coli serogroup O63, and in the second case a demonstration of the bioinformatics approach is done to E. coli serogroup O93. In the sixth chapter, a new version of the CarbBuilder software is presented. This includes a more robust building algorithm that helps build sterically crowded polysaccharide structures, as well as a general expansion of possible components. 

sted, utgiver, år, opplag, sider
Stockholm: Department of Organic Chemistry, Stockholm University, 2017. s. 65
Emneord
Carbohydrates, Bioinformatics, NMR Spectroscopy, Lipopolysaccharide, Glycosyltransferase, Computer-Assisted Structure Elucidation, O-antigen, Biosynthesis
HSV kategori
Forskningsprogram
organisk kemi
Identifikatorer
urn:nbn:se:su:diva-146867 (URN)978-91-7649-952-8 (ISBN)978-91-7649-953-5 (ISBN)
Disputas
2017-10-27, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, 10:00 (engelsk)
Opponent
Veileder
Merknad

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.

Tilgjengelig fra: 2017-10-04 Laget: 2017-09-13 Sist oppdatert: 2017-10-04bibliografisk kontrollert

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