Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

• characters of the PDB four-letter code. For convenience, the presentation of the database is hosted alongside the Privateer Web App [26]; the database part can be accessed at https://privateer.york.ac.uk/database or by navigating to the database icon on the top right of the screen. The website is dynamic and

NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform

• Luc Patiny,
• Hamed Musallam,
• Alejandro Bolaños,
• Michaël Zasso,
• Julien Wist,
• Metin Karayilan,
• Eva Ziegler,
• Johannes C. Liermann and
• Nils E. Schlörer

Beilstein J. Org. Chem. 2024, 20, 25–31, doi:10.3762/bjoc.20.4

• project website (as well as in the supplementary information) and is continuously extended. In addition, NMRium features online assistance with short movies. For teaching, the web-based nature makes the software an outstanding tool for live instruction: Steps demonstrated by the instructor may be

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• ganglioside biosynthesis, and altered ganglioside status in cancer, and the effects on network structure are predicted. The simulator is available at the Glycologue website, https://glycologue.org/. Keywords: gangliosides; Glycologue; glycosyltransferases; neuropathy; Svennerholm nomenclature; Introduction

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• specifying a particular sub-structure to retrieve structurally similar glycans (https://glytoucan.org/Structures/graphical). The software tool featured in the GlyTouCan website is called GlycanBuilder and is presented in a later section of our analysis. Recapitulating, SugarSketcher can be an efficient tool

• constructing 3D models of glycans from a sequence using standard nomenclature accessible at http://www.glycosciences.de/modeling/sweet2/doc/index.php (Figure 9, top). This tool is available as a part of the glycosciences.de website, which also provides other options for analysing glycans in three-dimensional

Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• available on the National Center for Functional Glycomics website (https://ncfg.hms.harvard.edu/protocols), for the multi-well chamber method (e.g., NCFG slides) and for the coverslip method (e.g., CFG slides). Data acquisition Once the slides are dried post sample incubation, the slides are scanned using a

• main website and database were created [33]. The microarray work was then taken over by the National Center for Functional Glycomics (NCFG) which was established in 2013. The CFG database has over 3000 experimental results files with 2 major types of arrays, the mammalian glycan printed array (noted as

• “Mammalian Printed Array” on the website and not to be confused with the “mammalian plate array” also present on the same page, which is not a microarray platform) and the pathogen array [34][35][36]. There are multiple versions of the mammalian glycan printed array (i.e., from v1 to v5.2) where each version

4-Hydroxy-3-methyl-2(1H)-quinolone, originally discovered from a Brassicaceae plant, produced by a soil bacterium of the genus Burkholderia sp.: determination of a preferred tautomer and antioxidant activity

• Dandan Li,
• Naoya Oku,
• Yukiko Shinozaki,
• Yoichi Kurokawa and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 1489–1494, doi:10.3762/bjoc.16.124

• partial sequence with a length of 800 bp (accession number LC508727) thus read was queried against the Basic Local Alignment Search Tool program (BLAST) available at the DNA Data Bank of Japan (DDBJ) website, which reported 99.9% homology to Burkholderia cepacia strain N1_1_43 (accession number MN691134

Anthelmintic drug discovery: target identification, screening methods and the role of open science

• Frederick A. Partridge,
• Ruth Forman,
• Carole J. R. Bataille,
• Graham M. Wynne,
• Marina Nick,
• Angela J. Russell,
• Kathryn J. Else and
• David B. Sattelle

Beilstein J. Org. Chem. 2020, 16, 1203–1224, doi:10.3762/bjoc.16.105

• enantiomer would be preferable for several reasons, for example, the inactive enantiomer has been linked to unwanted side-effects and also contributes a very bitter taste. With a view to finding a synthetic route to the active enantiomer, an open website was established, and several groups became involved

Opening up connectivity between documents, structures and bioactivity

• Christopher Southan

Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54

• followed by the IUPHAR Ion Channels Compendium of papers in 2003. This had developed into the IUPHAR-DB website by 2009 and was updated to the current IUPHAR/BPS Guide to Pharmacology (GtoPdb) by 2012 [10]. That same year also saw the first ChEMBL publication for which the website was live by 2010 [19

• PubChem SID 385612207 by GtoPdb is indexed in Entrez with a live PubChem link from the PubMed right hand facet. The arrow indicates the reciprocity in that users can navigate “in” to the system via GtoPdb or “out” either via the CID or the PMID. Statistics of GOSTAR (top row, from their website [15]) and

Recent advances on the transition-metal-catalyzed synthesis of imidazopyridines: an updated coverage

• Gagandeep Kour Reen,
• Ashok Kumar and
• Pratibha Sharma

Beilstein J. Org. Chem. 2019, 15, 1612–1704, doi:10.3762/bjoc.15.165

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• of selective anticancer peptide therapeutics. Keywords: breast cancer; decoralin; MCF-7 cells; peptide design; selective anticancer peptides; structure–activity relationships; Introduction Approximately 12% of U.S. women develop breast cancer according to the U.S. Breast Cancer website (http

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• with glycans from the GlycoMinds Ltd. seed database. Primary data of MS experiments and glycan array screens are also available via the CFG website. If a glycan structure has been detected to be bound by a glycan-binding protein in a CFG glycan array experiment, links to the corresponding protein pages

Looking forward to volume six

• Jonathan Clayden

Beilstein J. Org. Chem. 2010, 6, No. 1, doi:10.3762/bjoc.6.1

• developed specifically for BJOC to be organic chemistry specific, and is supported by a dedicated team at the Beilstein-Institut. The open access model allows us to be fully available to all users, and the number of people accessing our website and reading our papers is now over 20000 per month, an increase

• way within the journal, these papers can be viewed together using the “thematic series” tool on the website. Recent series have covered the topical themes of flow chemistry [1], supramolecular chemistry [2] and liquid crystals [3], and further series on carbohydrate chemistry and on organofluorine