GLYCO – Quantify Glycan Shielding of Glycosylated Proteins

GLYCO

:: DESCRIPTION

GLYCO (GLYcan COverage) is a program to calculate glycan coverage of glycoproteins (e.g., number of glycan atoms per protein surface residues/epitope residues).

::DEVELOPER

Myungjin Lee

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python

:: DOWNLOAD

GLYCO

:: MORE INFORMATION

Citation:

Lee M, Reveiz M, Rawi R, Kwong PD, Chuang GY.
GLYCO: a tool to quantify glycan shielding of glycosylated proteins.
Bioinformatics. 2021 Nov 23:btab791. doi: 10.1093/bioinformatics/btab791. Epub ahead of print. PMID: 34864901.

GECS – Glycan Structure Prediction from Microarray data

GECS

:: DESCRIPTION

GECS (Gene Expression to Chemical Structure) is a collection of prediction methods linking genomic or transcriptomic contents of genes to chemical structures of biosynthetic substances. This N-Glycan Prediction Server is based on the repertoire of glycosyltransferases for N-glycan biosynthesis.

::DEVELOPER

Kyoto University Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Genome Inform. 2007;18:237-46.
An improved scoring scheme for predicting glycan structures from gene expression data.
Suga A, Yamanishi Y, Hashimoto K, Goto S, Kanehisa M.

SimGlycan 5.94 – Glycan & Glycopeptide MS/MS Data Analysis Tool

SimGlycan 5.94

:: DESCRIPTION

SimGlycan® predicts the structure of glycans and glycopeptides using mass spectrometry data. SimGlycan® accepts the experimental MS/MS data generated by a mass spectrometer, matches them with its own database of theoretical fragments and generates a list of probable candidate structures.

::DEVELOPER

PREMIER Biosoft

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

SimGlycan Demo

:: MORE INFORMATION

Order SimGlycan

GUcal 1.2 – Capillary Electrophoresis based Glycan Analysis

GUcal 1.2

:: DESCRIPTION

GUcal is a software tool to automatically calculate the GU values of any peak of interest in a capillary electrophoresis separation of APTS labeled glycan samples also offering instant structural assignment by searching a built-in database.

::DEVELOPER

HAS-UP Translational Glycomic Research Group

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux / MacOS
MatLab

:: DOWNLOAD

GUcal

:: MORE INFORMATION

Citation:

GUcal: An integrated application for capillary electrophoresis based glycan analysis.
Jarvas G, Szigeti M, Guttman A.
Electrophoresis. 2015 Sep 18. doi: 10.1002/elps.201500397.

GS-align – Glycan Structure Alignment and Similarity Measurement

GS-align

:: DESCRIPTION

GS-align is a novel computational method for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition, and the optimal alignment is determined by the maximum structural similarity score, GS-score whose significance is size-independent.

::DEVELOPER

Wonpil Im Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

GS-align

:: MORE INFORMATION

Citation

GS-align for Glycan Structure Alignment and Similarity Measurement.
Lee HS, Jo S, Mukherjee S, Park SJ, Skolnick J, Lee J, Im W.
Bioinformatics. 2015 Apr 8. pii: btv202

KegDraw 0.1.15 beta – Draw Compound & Glycan Structures

KegDraw 0.1.15 beta

:: DESCRIPTION

KegDraw is a java application for drawing compound and glycan structures with capabilities to search against the KEGG databases.

::DEVELOPER

Kanehisa Laboratories

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac / Linux
Java

:: DOWNLOAD

KegDraw

:: MORE INFORMATION

Citation

Glycobiology. 2006 May;16(5):63R-70R. Epub 2005 Jul 13.
KEGG as a glycome informatics resource.
Hashimoto K, Goto S, Kawano S, Aoki-Kinoshita KF, Ueda N, Hamajima M, Kawasaki T, Kanehisa M.