SugarSketcher: Quick and Intuitive Online Glycan Drawing

被引：12

作者：

Alocci, Davide ^{[1
,2
]}

Suchankova, Pavla ^{[3
,4
]}

Costa, Renaud ^{[5
]}

Hory, Nicolas ^{[5
]}

Mariethoz, Julien ^{[1
,2
]}

Varekova, Radka Svobodova ^{[3
,4
]}

Toukach, Philip ^{[6
]}

Lisacek, Frederique ^{[1
,2
,7
]}

机构：

[1] SIB Swiss Inst Bioinformat, Proteome Informat Grp, CH-1211 Geneva, Switzerland

[2] Univ Geneva, Comp Sci Dept, CH-1211 Geneva, Switzerland

[3] Masaryk Univ Brno, CEITEC Cent European Inst Technol, Brno 62500, Czech Republic

[4] Natl Ctr Biomol Res, Fac Sci, Brno 62500, Czech Republic

[5] Polytech Nice Sophia, Campus SophiaTech, F-06903 Sophia Antipolis, France

[6] Russian Acad Sci, Lab Carbohydrate Chem, Zelinsky Inst Organ Chem, Moscow 119991, Russia

[7] Univ Geneva, Sect Biol, CH-1211 Geneva, Switzerland

来源：

MOLECULES | 2018年 / 23卷 / 12期

基金：

俄罗斯科学基金会;

关键词：

carbohydrate; 2D structure; software; SNFG notation; NOMENCLATURE; DATABASE; TOOL;

D O I：

10.3390/molecules23123206

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The quick mode allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The normal mode integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.

引用

页数：11

共 25 条

[1] Toolboxes for a standardised and systematic study of glycans [J].

Campbell, Matthew P. ;

Ranzinger, Rene ;

Luetteke, Thomas ;

Mariethoz, Julien ;

Hayes, Catherine A. ;

Zhang, Jingyu ;

Akune, Yukie ;

Aoki-Kinoshita, Kiyoko F. ;

Damerell, David ;

Carta, Giorgio ;

York, Will S. ;

Haslam, Stuart M. ;

Narimatsu, Hisashi ;

Rudd, Pauline M. ;

Karlsson, Niclas G. ;

Packer, Nicolle H. ;

Lisacek, Frederique .

BMC BIOINFORMATICS, 2014, 15

[2] The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures [J].

Ceroni, Alessio ;

Dell, Anne ;

Haslam, Stuart M. .

SOURCE CODE FOR BIOLOGY AND MEDICINE, 2007, 2 (01)

[3] DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information [J].

Cheng, Kai ;

Zhou, Yusen ;

Neelamegham, Sriram .

GLYCOBIOLOGY, 2017, 27 (03) :200-205

[4] GlycoSuiteDB: a curated relational database of glycoprotein glycan structures and their biological sources. 2003 update [J].

Cooper, CA ;

Joshi, HJ ;

Harrison, MJ ;

Wilkins, MR ;

Packer, NH .

NUCLEIC ACIDS RESEARCH, 2003, 31 (01) :511-513

[5] THE COMPLEX CARBOHYDRATE STRUCTURE DATABASE [J].

DOUBET, S ;

BOCK, K ;

SMITH, D ;

DARVILL, A ;

ALBERSHEIM, P .

TRENDS IN BIOCHEMICAL SCIENCES, 1989, 14 (12) :475-477

[6] POLYS 2.0: An Open Source Software Package for Building Three-Dimensional Structures of Polysaccharides [J].

Engelsen, Soren B. ;

Hansen, Peter I. ;

Perez, Serge .

BIOPOLYMERS, 2014, 101 (07) :733-743

[7] GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination [J].

Gotz, Lou ;

Abrahams, Jodie L. ;

Mariethoz, Julien ;

Rudd, Pauline M. ;

Karlsson, Niclas G. ;

Packer, Nicolle H. ;

Campbell, Matthew P. ;

Lisacek, Frederique .

BIOINFORMATICS, 2014, 30 (21) :3131-3133

[8] Proposal for a standard system for drawing structural diagrams of N- and O-linked carbohydrates and related compounds [J].

Harvey, David J. ;

Merry, Anthony H. ;

Royle, Louise ;

Campbell, Matthew P. ;

Dwek, Raymond A. ;

Rudd, Pauline M. .

PROTEOMICS, 2009, 9 (15) :3796-3801

[9] KEGG as a glycome informatics resource [J].

Hashimoto, K ;

Goto, S ;

Kawano, S ;

Aoki-Kinoshita, KF ;

Ueda, N ;

Hamajima, M ;

Kawasaki, T ;

Kanehisa, M .

GLYCOBIOLOGY, 2006, 16 (05) :63R-70R

[10] ChEBI in 2016: Improved services and an expanding collection of metabolites [J].

Hastings, Janna ;

Owen, Gareth ;

Dekker, Adriano ;

Ennis, Marcus ;

Kale, Namrata ;

Muthukrishnan, Venkatesh ;

Turner, Steve ;

Swainston, Neil ;

Mendes, Pedro ;

Steinbeck, Christoph .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D1214-D1219

← 1 2 3 →