CABANA Workshop: Resources and tools for target identification and drug discovery

Date:

 Wednesday 6 Friday 8 November 2019

Venue: 

IHEM - Instituto de Histología y Embriología - CCT CONICET Mendoza, Universidad Nacional de Cuyo, Faculty of Medical Sciences CONICET, CP 5500,  Mendoza,  Mendoza, Argentina

Application opens: 

Tuesday 24 September 2019

Application deadline: 

Sunday 06 October 2019

Participation: 

Open application with selection

Contact: 

Derrin Crawte, Maria Bernardi

Registration fee: 

$1200 ARS

Registration closed

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Course Overview

In this course, participants will learn the necessary theoretical background and basic tools of molecular target identification in pathogens and building of compound libraries for virtual screening. We also will introduce general concepts of molecular docking simulations.

 

Audience

This course is for biological researchers who want to learn more about the application of structural information in their work and how to use some of the key bioinformatics resources that are available.
 
Prerequisites
No previous experience in the field of structural bioinformatics is required, however a basic knowledge of protein structure would be of benefit.

Participants should be familiar with basic Linux operations - http://www.ee.surrey.ac.uk/Teaching/Unix/ - and have some experience of bioinformatics tools and databases.

Important: We strongly recommend participants bring their own laptop with Linux OS for the course.

Please also note: this course will be taught in Spanish, however the trainers are fluent in English and can offer language support where feasible.


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.
 

Learning outcomes

After this course you should be able to:

  • Describe how protein structure and molecular docking information can be applied to studies
  • Use the PDBe protein structure database
  • Identify potential protein targets using Target Pathogens
  • Build compound library using LigQ web server

 

Syllabus, Tools and Resources


During this course you will learn about: 

  • Protein structure databases (PDBe)
  • Introduction to protein structure interpretation and docking
  • Protein target identification using Target Pathogens (http://target.sbg.qb.fcen.uba.ar/patho/)
  • Homology modeling using Modeller
  • Binding site identification using FPocket
  • Compound library building using LigQ web server

Programme

Day 1 – Wednesday 6 November 2019
08:00-09:00 Arrival, registration  
09:00-10:00 Introduction to Next-Generation Sequencing (NGS) Ezequiel Sosa
10:00-11:00 Introduction to protein structure databases Ezequiel Sosa / Carlos Modenutti
11:00-11:30 Coffee break
11:30-13:00 Introduction to protein target identification in pathogens Ezequiel Sosa
13:00-14:00 Lunch
14:00-15:30 Protein target identification using Target Pathogens web server part 1 Ezequiel Sosa / Carlos Modenutti / Maria Bernardi
15:30-16:00 Coffee break  
16:00-17:30 Protein target identification using Target Pathogens web server part 2 Juan Blanco / Marcelo Gamarra  / Maria Bernardi
17:30 End of day 1  
Day 2 – Thursday 7 November 2019
09:00-10:00 Introduction to Homology Modeling  Juan Blanco
10:00-11:00 Introduction to Binding Site identification Ezequiel Sosa
11:00-11:30 Coffee break
11:30-13:00 Compounds databases and compounds library building Carlos Modenutti
13:00-14:00 Lunch
14:00-15:30 Homology modeling using Modeller and Binding Site identification using FPocket Juan Blanco / Marcelo Gamarra  / Maria Bernardi
15:30-16:00 Coffee break  
16:00-17:30 Compound library building using LigQ web server Ezequiel Sosa / Marcelo Gamarra  / Maria Bernardi
17:30 End of day 2  
Day 3 – Friday 8 November 2019
09:00-10:00 Introduction to molecular docking  Juan Blanco
10:00-11:00 Introduction to Solvent Site Biased Docking method Juan Blanco / Carlos Modenutti
11:00-11:30 Coffee break
11:30-13:00 Introduction to Virtual  Screening Carlos Modenutti
13:00-14:00 Lunch
14:00-16:00 Molecular Docking using Autodock4 and Autodock Vina Juan Blanco / Marcelo Gamarra  / Maria Bernardi
16:00-16:30 Coffee break  
16:30-17:30 Course close and feedback Course organizers
17:30 End of course