Programme

Overview of programme:
The autumn school will have two parts, both with a mixture of short lectures, presentations, hands-on exercises, and project work:

• the week starting 26 November 2012 at the Department of Bioinformatics, Centre of Medical Biotechnology, University of Duisburg-Essen, Campus Essen, Germany, will focus on methods based on physical models of biomolecular systems. Topics of this week include molecular dynamics simulation and related methods, biomolecular electrostatics, protein-protein-docking and matching, and datamining on sequences and structures;
• the week starting 3 December 2012 will deal with methods that make empirical knowledge available for modelling proteins. Topics of this week include homology modeling, ligand docking, computational solutions for structural analysis with X-ray, NMR, SAXS, or Cryo-EM. This part will take place at the Centre for Molecular and Biomolecular Informatics (CMBI) of the Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

Programme for both weeks:
Every day there will be seminars in the morning and hands-on practical session in the afternoon. Seminars start at 9:00 (except the Mondays when they start at 10:30). Hands-on sessions end late in the afternoon (except Fridays when they end at 16:00). Student presentations will take place at two evenings each of the two weeks.

Further details will be made available by October 4, 2012 at swift.cmbi.ru.nl/autumnschoolbioinformatics/.

Learning objectives (week in Essen):
After the course part in Essen, students will be able to:

• carry out molecular dynamics simulations of proteins,
• analyse molecular dynamics trajectories,
• compute and interpret electrostatics potentials of biomolecules,
• predict the structures of protein-protein complexes,
• find structures that are physico-chemically similar to a given epitope,
• compute statistical models that relate sequences to molecular function.

This ability will include scientific insight into underlying methods and their limitations, as well as use of software that implements these methods. All software used is either free and open source, or free to use over web services. In particular we will use:

• Gromacs for molecular dynamics: http://www.gromacs.org/,
• R for statistical analysis and datamining: http://www.r-project.org/,
• APBS for electrostatics: http://www.r-project.org/,
• EpitopeMatch for epitope matching: http://www.epitopematch.org/.

Learning objectives for the second week in Nijmegen
After the course part in Nijmegen, students will be able to:

• Visually inspect protein structures for a variety of topics
• Understand strengths and weaknesses of protein structures in relation to how they were solved
• Understand the (im)possibilities of homology modelling
• Apply everything learned during the course to problems of the real world.