MS tools
Other specialized Software Tools & Technologies
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NCBI provides several tools for downloading custom data sets. This page provides the option to download the software.
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For Description of uLIPSTIC Software, see this article. This software is described as recording cell-cell interaction. See the publication.
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PacBio sequencing technology has evolved to a different type of long read, known as highly accurate long reads, or HiFi reads. READ MORE for this 'Method of the year'
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Next-generation protein sequencing (NGPS) revolutionizes the comprehensive identification of all protein species within a single biological organism. READ MORE. Also, see here.
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For more accurate structure prediction of biomolecular interactions, one can use AlphaFold 3. However, not revealing the code has made it less useful for further research; See GEN article. Also see, OpenFold, a fast, memory efficient, and trainable implementation of AlphaFold 2.
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For other technologies, see here
Tools for Glycobioinformatics
List of commonly used specialized software tools for Mass Spectral Data analysis of Glycome (see: Publication, chapter 16 (page 323-375), for a short description)
BIONIC
For Glycopeptide identification, a Proprietary software (see: PMID: 23255153)
CARTOONIST
For MS analysis of glycan structure, a standalone tool software (see: Yu, CY., et. al., 2013)
GAGfinder
MS analysis specifically for GAGs, A standalone softwar (see: PMID: 29615495)
GAG-ID
MS analysis of heparin/heparan sulfate, a standalone software (see: PMID: 25887393)
GLYCOFOREST
LC-MS analysis of glycan, a standalone tool (see: Glycoforest 1.0)
GLYCOFRAGMENT
For MS analysis of glycan A part of glycosciences.de portal (see: Ref)
GLYCOANALYZER
Automated glycan annotation software from MS analysis data, a standalone software (see: PMID: 22903841)
Other Useful Tools
BRENDA
A Comprehensive Enzyme Information system; also provides structure-based search function.
GRITS Toolbox
A platform for glycomics data processing and archiving.
RHEA
It is an expert-curated knowledgebase of chemical and transport reactions of biological interest.