Introduction to Glycoinformatics (lectures and practicals) - streamed

Date 11 - 12 May 2020
Speaker(s) Frédérique Lisacek, Sylvie Ricard-Blum, Kiyoko Aoki-Kinoshita, Serge Perez, Raja Mazumder, Michael Tiemeyer, Julien Mariethoz et François Bonnardel
ECTS 0.5
Fees *academic: 120 CHF   -   for-profit: 600 CHF
Cancellation deadline 7 May 2020
City Streamed from Geneva, Grenoble, Lyon, Tokyo and Wa
*academic fee includes non for-profit organisations as well as unemployed participants at the time of application.

This course will be streamed only for the registered participants. Applications close on 7 May, and registered participants have to pay their registration fee immediately after receiving the confirmation email and thus confirm their participation.

If you are interested in attending only the lecture (lectures are free of charges), apply here.

Overview

Often enough the word glycoprotein is used yet the “glyco” part is hardly ever detailed. This is for instance the case with viruses in which surface spiking proteins are abbreviated GP and numbered like HIV GP120, but remain depicted as a smooth fist-like structure. In reality, glycan molecules decorate a broad variety of surface or secreted proteins and the literature is filled with unnoticed references focusing on the “glyco” part. This course is an opportunity to update and extend your knowledge of glycoproteins through the use of bioinformatics resources collectively called “glycoinformatics”. We will provide an overview of the challenging questions raised by the study of glycans as non-template driven molecules and the solutions that are currently proposed to store, search, analyse and visualise the effect(s) of protein glycosylation on protein structure, function(s) and interactions.

Audience

This course is addressed to any life scientist, from academia or industry: biologists, biochemists, from master students to advanced researchers.

Learning objectives

At the end of this course, the participants will be able to:

  • appreciate the importance of glycosylation and acquire the reflex of checking for known glycans when dealing with glycoproteins
  • know a range of useful glycoinformatics resources to investigate the potential for structural or functional changes
  • make more educated guesses regarding the feasibility of glycoprotein-protein interactions

Prerequisites

Knowledge / competencies

This course is designed for beginners in glycoinformatics or glycomics. Experience in using UniProt is required, and some basic knowledge about neXtProt and mass spectromety is recommended.

Technical

This course will be streamed, you are thus required to have your own computer with an internet connection.

Trainers

  • Frédérique Lisacek (FRL), University of Geneva and SIB, Switzerland
  • Sylvie Ricard-Blum (SRB), Université de Lyon, France
  • Kiyoko Aoki-Kinoshita KAK), Faculty of Science and Engineering, Soka University, Japan
  • Serge Perez (SEP), Centre de Recherches sur les Macromolécules Végétales (CERMAV) CNRS, Grenoble, France
  • Raja Mazumder (RAM), The George Washington University, Washington DC, USA
  • Michael Tiemeyer (MIT), The George Washington University, Washington DC, USA
  • Julien Mariethoz (JUM), University of Geneva and SIB, Switzerland
  • François Bonnardel (FRB), University of Geneva and SIB, Switzerland

Schedule

Day 1: 9am-12pm CET time zone - (lectures) - open to all viewers

  • Crash course in glycoscience (SEP)
  • The glycoinformatics landscape (FRL) (break)
  • Glycans and glycoproteins:
    • Introduction to glycomics@ExPASy (FRL)
    • Introduction to GlyCosmos (KAK)

Lunch break

1pm-2pm (lecture) - open to all viewers

  • Introduction to GlyGen (RAM, MIT)

2pm-3pm (hands on)

  • Tutorial: Glycan structure drawing software (FRL, KAK, JUM)
  • Tutorial: GlyTouCan (KAK)
  • Tutorial: GlyConnect (JUM, FRL)

3:30pm-5pm (hands on)

  • Analysing site-specific data and generating glycoprofiles (FRL)
  • Tutorial: Glynsight, Compozitor (JUM, FRL)
  • Introduction to 3D modelling from PDB (FRL, SEP)
  • Tutorial: Glycan 3D models (FRL, SEP, FRB)

Day 2:

9am-12pm CET time zone - (lectures) - open to all viewers

  • Glycan-binding proteins (FRL, FRB)
  • Glycosaminoglycans and proteoglycans (SRB) (break)
  • Glycan-protein interactions: a few practical examples (FRL, SRB)

Lunch break

1pm-3pm (hands on)

  • Tutorial: UniLectin (FRB)
  • Tutorial: interactions in 3D (SRB, FRB)
  • Tutorial: SugarBindDB, Glydin’ (FRL, JUM)

3:30pm-5pm (hands on)

  • Tutorial: MatrixDB (SRB, FRL)

Wrap-up

Venue and Time

This course will be streamed.

The course will start at 9:00 and end around 17:00.

Precise information will be provided to the participants on due time.

Application

The registration fees for academics are 120 CHF, and 600 CHF for participants from private companies.

Deadline for registration and free-of-charge cancellation is set to 7/05/2020. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

You will be informed by email of your registration confirmation.

If you are interested to attend the lectures only, apply here.

Additional information

Coordination: Patricia Palagi

We will recommend 0.5 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

For more information, please contact training@sib.swiss.