1
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Toukach P. Carbohydrate Structure Database: current state and recent developments. Anal Bioanal Chem 2024:10.1007/s00216-024-05383-w. [PMID: 38914734 DOI: 10.1007/s00216-024-05383-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/18/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024]
Abstract
Carbohydrate Structure Database (CSDB) is a curated glycan data collection and a glycoinformatic platform. In this report, its database, analytical, and other components that have appeared for the recent years are reviewed. The major improvements were achieving close-to-full coverage on glycans from microorganisms, launching modules for glycosyltransferases and saccharide conformations, online glycan builder and 3D modeler, NMR simulator, NMR-based structure predictor, and other tools.
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Affiliation(s)
- Philip Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia.
- Faculty of Chemistry, National Research University Higher School of Economics, Moscow, Russia.
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2
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Altmann F, Helm J, Pabst M, Stadlmann J. Introduction of a human- and keyboard-friendly N-glycan nomenclature. Beilstein J Org Chem 2024; 20:607-620. [PMID: 38505241 PMCID: PMC10949011 DOI: 10.3762/bjoc.20.53] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 02/27/2024] [Indexed: 03/21/2024] Open
Abstract
In the beginning was the word. But there were no words for N-glycans, at least, no simple words. Next to chemical formulas, the IUPAC code can be regarded as the best, most reliable and yet immediately comprehensible annotation of oligosaccharide structures of any type from any source. When it comes to N-glycans, the venerable IUPAC code has, however, been widely supplanted by highly simplified terms for N-glycans that count the number of antennae or certain components such as galactoses, sialic acids and fucoses and give only limited room for exact structure description. The highly illustrative - and fortunately now standardized - cartoon depictions gained much ground during the last years. By their very nature, cartoons can neither be written nor spoken. The underlying machine codes (e.g., GlycoCT, WURCS) are definitely not intended for direct use in human communication. So, one might feel the need for a simple, yet intelligible and precise system for alphanumeric descriptions of the hundreds and thousands of N-glycan structures. Here, we present a system that describes N-glycans by defining their terminal elements. To minimize redundancy and length of terms, the common elements of N-glycans are taken as granted. The preset reading order facilitates definition of positional isomers. The combination with elements of the condensed IUPAC code allows to describe even rather complex structural elements. Thus, this "proglycan" coding could be the missing link between drawn structures and software-oriented representations of N-glycan structures. On top, it may greatly facilitate keyboard-based mining for glycan substructures in glycan repositories.
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Affiliation(s)
| | - Johannes Helm
- Department of Chemistry, BOKU University, Vienna, Austria
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
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3
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Lundstrøm J, Urban J, Thomès L, Bojar D. GlycoDraw: a python implementation for generating high-quality glycan figures. Glycobiology 2023; 33:927-934. [PMID: 37498172 PMCID: PMC10859633 DOI: 10.1093/glycob/cwad063] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/14/2023] [Accepted: 07/26/2023] [Indexed: 07/28/2023] Open
Abstract
Glycans are essential to all scales of biology, with their intricate structures being crucial for their biological functions. The structural complexity of glycans is communicated through simplified and unified visual representations according to the Symbol Nomenclature for Glycans (SNFGs) guidelines adopted by the community. Here, we introduce GlycoDraw, a Python-native implementation for high-throughput generation of high-quality, SNFG-compliant glycan figures with flexible display options. GlycoDraw is released as part of our glycan analysis ecosystem, glycowork, facilitating integration into existing workflows by enabling fully automated annotation of glycan-related figures and thus assisting the analysis of e.g. differential abundance data or glycomics mass spectra.
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Affiliation(s)
- Jon Lundstrøm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
| | - James Urban
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
| | - Luc Thomès
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
| | - Daniel Bojar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Medicinaregatan 9C, 41390 Gothenburg, Västra Götaland, Sweden
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4
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Mariethoz J, Alocci D, Karlsson NG, Packer NH, Lisacek F. An Interactive View of Glycosylation. Methods Mol Biol 2022; 2370:41-65. [PMID: 34611864 DOI: 10.1007/978-1-0716-1685-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The present chapter focuses on the interactive and explorative aspects of bioinformatics resources that have been recently released in glycobiology. The comparative analysis of data in a field where knowledge is scattered, incomplete, and disconnected from main biology requires efficient visualization, integration, and interactive tools that are currently only partially implemented. This overview highlights converging efforts toward building a consistent picture of protein glycosylation.
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Affiliation(s)
- Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
- Computer Science Department, University of Geneva, Geneva, Switzerland
| | - Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Nicolle H Packer
- Department of Molecular Sciences and ARC Centre of Excellence for Nanoscale Biophotonics, Macquarie University, Sydney, NSW, Australia
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, University of Geneva, Geneva, Switzerland.
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5
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SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures. Molecules 2021; 26:molecules26237149. [PMID: 34885724 PMCID: PMC8659005 DOI: 10.3390/molecules26237149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/17/2022] Open
Abstract
In life science fields, database integration is progressing and contributing to collaboration between different research fields, including the glycosciences. The integration of glycan databases has greatly progressed collaboration worldwide with the development of the international glycan structure repository, GlyTouCan. This trend has increased the need for a tool by which researchers in various fields can easily search glycan structures from integrated databases. We have developed a web-based glycan structure search tool, SugarDrawer, which supports the depiction of glycans including ambiguity, such as glycan fragments which contain underdetermined linkages, and a database search for glycans drawn on the canvas. This tool provides an easy editing feature for various glycan structures in just a few steps using template structures and pop-up windows which allow users to select specific information for each structure element. This tool has a unique feature for selecting possible attachment sites, which is defined in the Symbol Nomenclature for Glycans (SNFG). In addition, this tool can input and output glycans in WURCS and GlycoCT formats, which are the most commonly-used text formats for glycan structures.
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Bochkov AY, Toukach PV. CSDB/SNFG Structure Editor: An Online Glycan Builder with 2D and 3D Structure Visualization. J Chem Inf Model 2021; 61:4940-4948. [PMID: 34595926 DOI: 10.1021/acs.jcim.1c00917] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This article describes features, usage, and application of an CSDB/SNFG Structure Editor, a new online tool for quick and intuitive input of carbohydrate and derivative structures using Symbol Nomenclature for Glycans (SNFG). The Editor is built on a platform of the Carbohydrate Structure Database (CSDB) and relies on its online services via the dedicated web-API. The Editor allows building of oligo- and polymeric glycan structures and supports most features of natural glycans, such as underdetermined structures, alternative branches, repeating subunits, SMILES specification of atypical monomers, and others. The vocabulary of building blocks contains 600+ monomeric residues, including 327 monosaccharides. Support for SMILES allows input and visualization of chemical structures of virtually unlimited complexity. On the other hand, the interface follows the recognized GlycanBuilder style easy to novice users. The export feature includes support for CSDB Linear, GlycoCT, WURCS, SweetDB, and Glycam notations, SMILES codes, MOL/PDB atomic coordinate formats, raster and vector SNFG images, and on-the-fly visualization as 2D structural formulas and 3D molecular models. Integration of the Editor into any web-based glycoinformatics project is straightforward and simple, similarly to any other modern JavaScript application.
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Affiliation(s)
- Andrei Y Bochkov
- Laboratory of Carbohydrate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russia
| | - Philip V Toukach
- Laboratory of Carbohydrate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow, Russia.,Faculty of Chemistry, National Research University Higher School of Economics, Vavilova 7, 117312 Moscow, Russia
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7
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Mehta AY, Cummings RD. GlycoGlyph: a glycan visualizing, drawing and naming application. Bioinformatics 2020; 36:3613-3614. [PMID: 32170934 DOI: 10.1093/bioinformatics/btaa190] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Glycan structures are commonly represented using symbols or linear nomenclature such as that from the Consortium for Functional Glycomics (also known as modified IUPAC-condensed nomenclature). No current tool allows for writing the name in such format using a graphical user interface (GUI); thus, names are prone to errors or non-standardized representations. RESULTS Here we present GlycoGlyph, a web application built using JavaScript, which is capable of drawing glycan structures using a GUI and providing the linear nomenclature as an output or using it as an input in a dynamic manner. GlycoGlyph also allows users to save the structures as an SVG vector graphic, and allows users to export the structure as condensed GlycoCT. AVAILABILITY AND IMPLEMENTATION The application can be used at: https://glycotoolkit.com/Tools/GlycoGlyph/. The application is tested to work in modern web browsers such as Firefox or Chrome. CONTACT aymehta@bidmc.harvard.edu or rcummin1@bidmc.harvard.edu.
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Affiliation(s)
- Akul Y Mehta
- Department of Surgery, National Center for Functional Glycomics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Richard D Cummings
- Department of Surgery, National Center for Functional Glycomics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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Lal K, Bermeo R, Perez S. Computational tools for drawing, building and displaying carbohydrates: a visual guide. Beilstein J Org Chem 2020; 16:2448-2468. [PMID: 33082879 PMCID: PMC7537382 DOI: 10.3762/bjoc.16.199] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 09/17/2020] [Indexed: 01/08/2023] Open
Abstract
Drawing and visualisation of molecular structures are some of the most common tasks carried out in structural glycobiology, typically using various software. In this perspective article, we outline developments in the computational tools for the sketching, visualisation and modelling of glycans. The article also provides details on the standard representation of glycans, and glycoconjugates, which helps the communication of structure details within the scientific community. We highlight the comparative analysis of the available tools which could help researchers to perform various tasks related to structure representation and model building of glycans. These tools can be useful for glycobiologists or any researcher looking for a ready to use, simple program for the sketching or building of glycans.
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Affiliation(s)
- Kanhaya Lal
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, I-20133, Italy
| | - Rafael Bermeo
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, I-20133, Italy
| | - Serge Perez
- Univ. Grenoble Alpes, CNRS, CERMAV, 38000 Grenoble, France
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Neelamegham S, Aoki-Kinoshita K, Bolton E, Frank M, Lisacek F, Lütteke T, O'Boyle N, Packer NH, Stanley P, Toukach P, Varki A, Woods RJ. Updates to the Symbol Nomenclature for Glycans guidelines. Glycobiology 2020; 29:620-624. [PMID: 31184695 DOI: 10.1093/glycob/cwz045] [Citation(s) in RCA: 279] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/15/2019] [Accepted: 06/06/2019] [Indexed: 11/14/2022] Open
Abstract
The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard for the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It is hosted by the National Center for Biotechnology Information (NCBI) at the NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to the SNFG page in the past year to update the rules for depicting glycans using the SNFG, to include more examples of use, particularly for non-mammalian organisms, and to provide guidelines for the depiction of ambiguous glycan structures. This Glycoforum article summarizes these recent changes.
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Affiliation(s)
- Sriram Neelamegham
- Department of Chemical & Biological Engineering and Medicine, State University of New York, 906 Furnas Hall, Buffalo, NY 14260, USA
| | - Kiyoko Aoki-Kinoshita
- Glycan & Life System Integration Center (GaLSIC), Faculty of Science and Engineering, Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - Evan Bolton
- National Library of Medicine, 8600 Rockville Pike, Bldg. 38A, Room 8S810, Bethesda, MD 20896, USA
| | - Martin Frank
- Biognos AB, Generatorsgatan 1 / Box 8963, 402 74 Göteborg, Sweden
| | - Frederique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Computer Science Department, University of Geneva, route de Drize 7, CH - 1227 Geneva Switzerland, and also Section of Biology, University of Geneva, Geneva, Switzerland
| | - Thomas Lütteke
- GIP GmbH, Strahlenberger Str. 112, 63067 Offenbach, Germany
| | - Noel O'Boyle
- NextMove Software, Innovation Centre, Cambridge Science Park, Milton Road, Cambridge, CB4 0EY, UK
| | - Nicolle H Packer
- Department of Molecular Sciences, Faculty of Science & Engineering, Rm 307, Building E8C, Macquarie University, Sydney, NSW 2109, Australia
| | - Pamela Stanley
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave, New York, NY, 10461, USA
| | - Philip Toukach
- Laboratory of Carbohydrate Chemistry, Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. 119991 Moscow, Leninsky prospect 47, Russia
| | - Ajit Varki
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
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Toukach PV, Egorova KS. New Features of Carbohydrate Structure Database Notation (CSDB Linear), As Compared to Other Carbohydrate Notations. J Chem Inf Model 2019; 60:1276-1289. [DOI: 10.1021/acs.jcim.9b00744] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosect 47, Moscow, Russia 119991
- National Research University Higher School of Economics, Myasnitskaya 20, Moscow, Russia 101000
| | - Ksenia S. Egorova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosect 47, Moscow, Russia 119991
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12
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Alocci D, Mariethoz J, Gastaldello A, Gasteiger E, Karlsson NG, Kolarich D, Packer NH, Lisacek F. GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical. J Proteome Res 2018; 18:664-677. [DOI: 10.1021/acs.jproteome.8b00766] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Davide Alocci
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Julien Mariethoz
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Alessandra Gastaldello
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
| | - Elisabeth Gasteiger
- Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CH-1211 Geneva, Switzerland
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, Sydney, New South Wales 2109, Australia
| | - Nicolle H. Packer
- Institute for Glycomics, Griffith University, Southport, Queensland 4215, Australia
- ARC Centre for Nanoscale BioPhotonics, Macquarie University and Griffith University, Sydney, New South Wales 2109, Australia
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Frédérique Lisacek
- Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Rue Michel-Servet 1, CH-1211 Geneva, Switzerland
- Computer Science Department, University of Geneva, CH-1227 Geneva, Switzerland
- Section of Biology, University of Geneva, CH-1211 Geneva, Switzerland
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