Course outside EMBL-EBI

CABANA Workshop: Chemoinformatics in Drug Discovery

The aim of this workshop is to introduce researchers to the field of Chemoinformatics, especially in the areas of Structure-Based Drug Design (SBDD) and Ligand-Based Drug Design (LBDD). Trainees will cover the use of protein, ligand and drug databases, protein modelling, molecular docking and virtual screening for drug discovery applications. Managing and analysing virtual chemical libraries will also be covered, including the application of machine learning algorithms in drug discovery.


The workshop will be instructed by trainers from the University of Antioquia in Colombia, from CINVESTAV Unit for Advanced Genomics (LANGEBIO) in Mexico, as well as local expert researchers from the School of Chemistry at the National Autonomous University of Mexico (UNAM).

Who is this course for?

This workshop is suitable for researchers working in Latin American countries. Early career researchers, including graduate students, postdocs and professors working, or planning to start working in Chemoinformatics, are warmly encouraged to apply.


This workshop will be located in a room with computers however we recommend participants bring their own laptops.

A number of travel fellowships are available for this course - early-stage researchers and researchers from underrepresented groups are especially encouraged to apply for CABANA travel fellowships. You can apply for travel fellowships via the course application form.

Prerequisites: 
Undergraduate-level knowledge of chemical and protein structures are required. Familiarity with basic chemoinformatics concepts and notions of programming (R, Python and/or UNIX) are recommended. Please note this course will be taught in English, however, the trainers are fluent in Spanish and can offer language support where needed.

What will I learn?

Learning outcomes

After this course, you should be able to:

  • Visualize proteins and ligands using molecular visualization tools
  • Browse and investigate biomolecular structural information using PDBe
  • Use molecular docking and virtual screening for hit identification
  • Apply homology modelling to the prediction of protein structures
  • Apply predictive models (regressions, classifications) to molecules
Course content

During this course you will learn about: 

  • Protein Databank in Europe (PDBe) resources
  • Molecular visualization tools such as PyMol
  • DataWarrior
  • Homology modelling using MODELLER, molecular docking and virtual screening
  • BIOFACQUIM compound database
  • Machine learning algorithms and statistics for drug discovery

Trainers

Fabien Plisson
LANGEBIO, Cinvestav, Mexico
Jose Medina-Franco
School of Chemistry, UNAM, Mexico
Rodrigo Ochoa Deossa
EMBL-EBI, UK
Barbara Diaz
UNAM, Mexico
Edgar Lopez
UNAM, Mexico

Programme

Day 1 – Tuesday 15 October 2019
08:30-09:00 Arrival and registration  
09:00-10:00 Welcome and introductions Organizers
10:00-11:00 Public Seminar at Langebio: “SBDD and LBDD approaches in drug discovery to neglected tropical diseases” Rodrigo Ochoa
11:00-11:30 Coffee Break
11:30-12:30 Introduction to Chemoinformatics José Medina-Franco
12:30-13:30 Lunch
13:30-15:00 Introduction to PDBe (proteins) and PyMOL Rodrigo Ochoa / Fabien Plisson
15:00-16:00 Introduction to ChEMBL/ZINC (compounds) and DataWarrior Rodrigo Ochoa
16:00-16:30 Coffee Break  
16:30-17:30 ChEMBL/ZINC (compounds) and DataWarrior practical Rodrigo Ochoa
17:30 End of day 1  
Day 2 – Wednesday 16 October 2019
09:00-11:00 Introduction to Structure-based drug discovery and molecular docking José Medina-Franco
11:00-11:30 Coffee Break
11:30-13:00 Practical in Virtual Screening Fabien Plisson / JMF team
13:00-14:00 Lunch
14:00-15:30 Homology Modelling and Practical  Rodrigo Ochoa
15:30-16:00 Coffee Break  
16:00-17:00 Modeller Practical continued Rodrigo Ochoa
17:00 End of day 2  
Day 3 – Thursday 17 October 2019
09:00-10:00 Introduction to Ligand-based drug discovery Fabien Plisson
10:00-11:00 Calculations of physicochemical descriptors with DataWarrior JMF team
11:00-11:30 Coffee Break
11:30-13:00 Unsupervised Learning: PCA, SOMs, t-SNE, boxplots Fabien Plisson
13:00-14:00 Lunch
14:00-15:30 Practical in BIOFACQUIM vs the world JMF team
16:00-22:00 Excursion to Guanajuato, event dinner  
22:00 End of day 3  
Day 4 – Friday 18 October 2019
09:00-10:00 Introduction to QSAR and Machine Learning algorithms in Drug discovery Fabien Plisson
10:00-11:00 Supervised Learning: Regressions Fabien Plisson
11:00-11:30 Coffee Break
11:30-13:00 Practical in regressions with R/R Studio JMF team / Fabien Plisson
13:00-14:00 Lunch
14:00-15:30 Supervised Learning: Classifications Fabien Plisson
15:30-16:00 Coffee Break
16:00-17:00 Practical in Classifications JMF team / Fabien Plisson
17:00-17:30 End of Course – Wrap-up and feedback Organizers

In order to be considered for a place on this course applicants must complete the online application form.

Incomplete applications will NOT be considered. 

If you have any queries about the registration process please email Guilherme Oliveira and Piv Gopalasingam.

Please note that the registration fee of $800 MXN includes:

  • Lunches and refreshment breaks
  • Accommodation for 5 nights (14-18 Oct)
  • Course materials 
  • Course dinner on Thursday, October 17th
  • Course certificate
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Course materials

15 - 18 October 2019
LANGEBIO, Cinvestav Mexico
MXN $800
Contact
Derrin Crawte

Organisers
  • Fabien Plisson
    LANGEBIO, Cinvestav, Mexico
  • Jose Medina-Franco
    School of Chemistry, UNAM, Mexico
  • Piraveen Gopalasingam
    EMBL-EBI, UK

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