Literature DB >> 33125071

The international glycan repository GlyTouCan version 3.0.

Akihiro Fujita1, Nobuyuki P Aoki1, Daisuke Shinmachi1, Masaaki Matsubara2, Shinichiro Tsuchiya2, Masaaki Shiota1, Tamiko Ono1, Issaku Yamada2, Kiyoko F Aoki-Kinoshita1,3.   

Abstract

Glycans serve important roles in signaling events and cell-cell communication, and they are recognized by lectins, viruses and bacteria, playing a variety of roles in many biological processes. However, there was no system to organize the plethora of glycan-related data in the literature. Thus GlyTouCan (https://glytoucan.org) was developed as the international glycan repository, allowing researchers to assign accession numbers to glycans. This also aided in the integration of glycan data across various databases. GlyTouCan assigns accession numbers to glycans which are defined as sets of monosaccharides, which may or may not be characterized with linkage information. GlyTouCan was developed to be able to recognize any level of ambiguity in glycans and uniquely assign accession numbers to each of them, regardless of the input text format. In this manuscript, we describe the latest update to GlyTouCan in version 3.0, its usage, and plans for future development.
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Entities:  

Year:  2021        PMID: 33125071      PMCID: PMC7779025          DOI: 10.1093/nar/gkaa947

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  8 in total

1.  Publishing on the semantic web.

Authors:  T Berners-Lee; J Hendler
Journal:  Nature       Date:  2001-04-26       Impact factor: 49.962

2.  WURCS 2.0 Update To Encapsulate Ambiguous Carbohydrate Structures.

Authors:  Masaaki Matsubara; Kiyoko F Aoki-Kinoshita; Nobuyuki P Aoki; Issaku Yamada; Hisashi Narimatsu
Journal:  J Chem Inf Model       Date:  2017-03-22       Impact factor: 4.956

3.  GlyTouCan: an accessible glycan structure repository.

Authors:  Michael Tiemeyer; Kazuhiro Aoki; James Paulson; Richard D Cummings; William S York; Niclas G Karlsson; Frederique Lisacek; Nicolle H Packer; Matthew P Campbell; Nobuyuki P Aoki; Akihiro Fujita; Masaaki Matsubara; Daisuke Shinmachi; Shinichiro Tsuchiya; Issaku Yamada; Michael Pierce; René Ranzinger; Hisashi Narimatsu; Kiyoko F Aoki-Kinoshita
Journal:  Glycobiology       Date:  2017-10-01       Impact factor: 4.313

4.  The GlyCosmos Portal: a unified and comprehensive web resource for the glycosciences.

Authors:  Issaku Yamada; Masaaki Shiota; Daisuke Shinmachi; Tamiko Ono; Shinichiro Tsuchiya; Masae Hosoda; Akihiro Fujita; Nobuyuki P Aoki; Yu Watanabe; Noriaki Fujita; Kiyohiko Angata; Hiroyuki Kaji; Hisashi Narimatsu; Shujiro Okuda; Kiyoko F Aoki-Kinoshita
Journal:  Nat Methods       Date:  2020-07       Impact factor: 28.547

5.  GlycoCT-a unifying sequence format for carbohydrates.

Authors:  S Herget; R Ranzinger; K Maass; C-W V D Lieth
Journal:  Carbohydr Res       Date:  2008-03-13       Impact factor: 2.104

Review 6.  Implementation of linked data in the life sciences at BioHackathon 2011.

Authors:  Kiyoko F Aoki-Kinoshita; Akira R Kinjo; Mizuki Morita; Yoshinobu Igarashi; Yi-An Chen; Yasumasa Shigemoto; Takatomo Fujisawa; Yukie Akune; Takeo Katoda; Anna Kokubu; Takaaki Mori; Mitsuteru Nakao; Shuichi Kawashima; Shinobu Okamoto; Toshiaki Katayama; Soichi Ogishima
Journal:  J Biomed Semantics       Date:  2015-01-07

Review 7.  Towards a standardized bioinformatics infrastructure for N- and O-glycomics.

Authors:  Miguel A Rojas-Macias; Julien Mariethoz; Peter Andersson; Chunsheng Jin; Vignesh Venkatakrishnan; Nobuyuki P Aoki; Daisuke Shinmachi; Christopher Ashwood; Katarina Madunic; Tao Zhang; Rebecca L Miller; Oliver Horlacher; Weston B Struwe; Yu Watanabe; Shujiro Okuda; Fredrik Levander; Daniel Kolarich; Pauline M Rudd; Manfred Wuhrer; Carsten Kettner; Nicolle H Packer; Kiyoko F Aoki-Kinoshita; Frédérique Lisacek; Niclas G Karlsson
Journal:  Nat Commun       Date:  2019-07-22       Impact factor: 14.919

8.  GlycanFormatConverter: a conversion tool for translating the complexities of glycans.

Authors:  Shinichiro Tsuchiya; Issaku Yamada; Kiyoko F Aoki-Kinoshita
Journal:  Bioinformatics       Date:  2019-07-15       Impact factor: 6.937

  8 in total
  11 in total

1.  RCSB Protein Data Bank: Celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D.

Authors:  Stephen K Burley; Charmi Bhikadiya; Chunxiao Bi; Sebastian Bittrich; Li Chen; Gregg V Crichlow; Jose M Duarte; Shuchismita Dutta; Maryam Fayazi; Zukang Feng; Justin W Flatt; Sai J Ganesan; David S Goodsell; Sutapa Ghosh; Rachel Kramer Green; Vladimir Guranovic; Jeremy Henry; Brian P Hudson; Catherine L Lawson; Yuhe Liang; Robert Lowe; Ezra Peisach; Irina Persikova; Dennis W Piehl; Yana Rose; Andrej Sali; Joan Segura; Monica Sekharan; Chenghua Shao; Brinda Vallat; Maria Voigt; John D Westbrook; Shamara Whetstone; Jasmine Y Young; Christine Zardecki
Journal:  Protein Sci       Date:  2021-11-06       Impact factor: 6.725

2.  Functions of Glycosylation and Related Web Resources for Its Prediction.

Authors:  Kiyoko F Aoki-Kinoshita
Journal:  Methods Mol Biol       Date:  2022

3.  GlyNet: a multi-task neural network for predicting protein-glycan interactions.

Authors:  Eric J Carpenter; Shaurya Seth; Noel Yue; Russell Greiner; Ratmir Derda
Journal:  Chem Sci       Date:  2022-05-16       Impact factor: 9.969

4.  In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis.

Authors:  Andrew G McDonald; Julien Mariethoz; Gavin P Davey; Frédérique Lisacek
Journal:  Sci Rep       Date:  2022-06-27       Impact factor: 4.996

5.  CarboGrove: a resource of glycan-binding specificities through analyzed glycan-array datasets from all platforms.

Authors:  Zachary L Klamer; Chelsea M Harris; Jonathan M Beirne; Jessica E Kelly; Jian Zhang; Brian B Haab
Journal:  Glycobiology       Date:  2022-07-13       Impact factor: 5.954

6.  Circulating Glycan Monosaccharide Composite-Based Biomarker Diagnoses Colorectal Cancer at Early Stages and Predicts Prognosis.

Authors:  Haoran Li; Xueling Wang; Xiaodan Huang; Yanli He; Yiran Zhang; Cui Hao; Pengjiao Zeng; Meng Zhang; Yanyun Gao; Dandan Yang; Ming Shan; Huaiqian Dou; Xiaoyu Li; Xiaotian Chang; Zibin Tian; Lijuan Zhang
Journal:  Front Oncol       Date:  2022-04-29       Impact factor: 5.738

7.  The 2021 Nucleic Acids Research database issue and the online molecular biology database collection.

Authors:  Daniel J Rigden; Xosé M Fernández
Journal:  Nucleic Acids Res       Date:  2021-01-08       Impact factor: 16.971

8.  Dealing with the Ambiguity of Glycan Substructure Search.

Authors:  Vincenzo Daponte; Catherine Hayes; Julien Mariethoz; Frederique Lisacek
Journal:  Molecules       Date:  2021-12-23       Impact factor: 4.411

9.  SugarDrawer: A Web-Based Database Search Tool with Editing Glycan Structures.

Authors:  Shinichiro Tsuchiya; Masaaki Matsubara; Kiyoko F Aoki-Kinoshita; Issaku Yamada
Journal:  Molecules       Date:  2021-11-25       Impact factor: 4.411

10.  The glycoconjugate ontology (GlycoCoO) for standardizing the annotation of glycoconjugate data and its application.

Authors:  Issaku Yamada; Matthew P Campbell; Nathan Edwards; Leyla Jael Castro; Frederique Lisacek; Julien Mariethoz; Tamiko Ono; Rene Ranzinger; Daisuke Shinmachi; Kiyoko F Aoki-Kinoshita
Journal:  Glycobiology       Date:  2021-08-07       Impact factor: 5.954

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