The Gulbenkian Training Programme in Bioinformatics
Pharmacogenomics: new opportunities for drug discovery PGDD08 - course websiteIMPORTANT DATESDeadline 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;
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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 |
Instituto Gulbenkian de Ciência,
Apartado14, 2781-901 Oeiras, Portugal