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
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.
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.
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.
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
Day 1 – Wednesday 6 November 2019
|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|
|11:30-13:00||Introduction to protein target identification in pathogens||Ezequiel Sosa|
|14:00-15:30||Protein target identification using Target Pathogens web server part 1||Ezequiel Sosa / Carlos Modenutti / Maria Bernardi|
|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|
|11:30-13:00||Compounds databases and compounds library building||Carlos Modenutti|
|14:00-15:30||Homology modeling using Modeller and Binding Site identification using FPocket||Juan Blanco / Marcelo Gamarra / Maria Bernardi|
|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|
|11:30-13:00||Introduction to Virtual Screening||Carlos Modenutti|
|14:00-16:00||Molecular Docking using Autodock4 and Autodock Vina||Juan Blanco / Marcelo Gamarra / Maria Bernardi|
|16:30-17:30||Course close and feedback||Course organizers|
|17:30||End of course|