GTPB

The Gulbenkian Training Programme in Bioinformatics


GTPB runs at the Instituto Gulbenkian de Ciência on a yearly basis since 1999.
More than 1200 course attendees in 9 years
Pedro Fernandes, GTPB organizer



Pharmacogenomics:

new opportunities for drug discovery

PGDD08 - course website

IMPORTANT DATES
Deadline for applications: October 10th 2008
Course date: November 3rd - November 7th 2008


Instructors:

Marc A. Marti-Renom
has 14 years of experience in international academic institutions. Since July 2006 Head of the Structural Genomics Unit at the CIPF, Valencia (Spain). He obtained his Ph.D. in January 1999 under the supervision of Profs. Martin Karplus, Francesc X. Aviles, and Baldomero Oliva. He was Postdoctoral Fellow and Research Associate at the Rockefeller University (1999-2003). Assistant Adjunct Professor at the University of California at San Francisco (2003-2006). Key personnel in three funded NIH grants. Member of the Admissions Committee at the School of Pharmacy at UCSF (2003-2006). Up-to-date, his research has resulted in 39 peer-reviewed articles, 2 invited reviews, 9 book chapters and 12 invited presentations in international conferences. He has directed the development of two major software packages (EVA-CM and DBAli) as well as has significantly contributed to the MODBASE, MODPIPE and MODELLER software packages. Detailed information about his research can be found at http://sgu.bioinfo.cipf.es.
Centro de Investigación Príncipe Felipe. Valencia. Spain.
Antonio Pineda-Lucena got his PhD at the Centro de Investigaciones Biologicas (CSIC, Madrid, Spain) in 1995. After that, he moved to the Netherlands (EMBO and Marie Curie fellowships) to work as a postdoctoral researcher with Prof. Dr. Cees Hilbers at the University of Nijmegen. Later on, he got a position as an Associate Scientist at the Ontario Cancer Institute in Toronto (Canada), the canadian reference centre for cancer treatment, where he was working in the structural characterization of oncoproteins and tumor suppressors, as well as in the development of new technologies for structural genomics. Two years later, he accepted a position in one of the biggest pharmaceutical companies, AstraZeneca (Manchester, UK). APL joined the Centro de Investigacion Principe Felipe (CIPF) in February, 2005 to head the Laboratory of Structural Biology and the NMR facility. The group has three other members (a Ramon y Cajal senior researcher, three postdoctoral researchers and a technician), with experience in NMR, organic chemistry, cell biology, microbiology, protein chemistry, computational chemistry, cheminformatics and drug design using fragment-based screening.
Centro de Investigación Príncipe Felipe. Valencia. Spain.


Course Description

During the five days of the course, we will teach several topics relevant to structure-based drug discovery. Such topics include structure determination and prediction (days 1 and 2), human variability and pharmacogenomics (day 3), docking of small molecules from an experimental and computational perspective (day 4) and quantitative structure-activity relationships (day 5). This course is addressed to students with some knowledge of structural biology as well as computational biology. However, the course aims to introducethe students to the theoretical background as well as some practical applications. Attendees will be trained in software for: protein structure determination from NMR; structure prediction by MODELLER; SNP analysis; docking of small molecules by DOCK; QSAR analysis and generation of ligand libraries;

Topics covered:
Protein Structure Determination
Protein Structure Prediction
SNP Variability and Disease
Docking of Small Molecules
QSAR. Quantitative structure-activity relationships


Timetable:

November 3rd

Day 1

09:30 -11:00

Structure-based drug design

11:00 -11:30

Coffee Break

11:30 -12:30

Protein structure determination

12:30 - 14:00

Lunch Break

14:00 - 16:00

PYMOL, PDBSUM

16:00 - 16:30

Tea Break

16:30 - 18:00

PDBBIND DATABASE, LIGANDINFO-CNIO

November 4th

Day 2

09:30 -11:00

Template search and Target-template alignment

11:00 - 11:30

Coffee Break

11:30 - 12:30

Model building and model assessment.

12:30 - 14:00

Lunch Break

14:00 - 16:00

MODELLER basic example

16:00 - 16:30

Tea Break

16:30 - 18:00

MODELLER your own example or advanced example.

November 5th

Day 3

09:30 -11:00

Single Nucleotide Porlymorfism & Binding site prediction

11:00 - 11:30

Coffee Break

11:30 - 12:30

Protein-Ligand Docking with AutoDock

12:30 - 14:00

Lunch Break

14:00 - 16:00

AutoDock tutorial

16:00 - 16:30

Tea Break

16:30 - 18:00

AutoDock tutorial

November 6th

Day 4

09:30 -11:00

Chemical libraries, Pharmacophore analysis

11:00 -11:30

Coffee Break

11:30 -12:30

QSAR introduction

12:30 - 14:00

Lunch Break

14:00 - 16:00

SMILES, PUBCHEM, DRUGBANK, ZINC

16:00 - 16:30

Tea Break

16:30 - 18:00

LIGAND.INFO, LIGANDSCOUT

November 7th

Day 5

09:30 -18:00

Practical application to the HIV drug resistance


Pre-requisites: Basic Molecular Biology and Biochemistry. Elementary computing skills. Some basic knowledge of structural biology as well as computational biology

GTPB Details

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Instituto Gulbenkian de Ciência, Apartado14, 2781-901 Oeiras, Portugal


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Last updated:September 26th 2008