EMBO course on biomolecular simulation 18-25 July 2004.
NOTE: the course is very much overbooked. We were forced to
reject many good applications. All accepted participants have
been notified directly by email.
Molecular simulation techniques have never been as accessible and as valuable
to biologists as they are now. The function of biological macromolecules is
determined by their three-dimensional structure and dynamics. Knowledge of the
structure is necessary for understanding their mechanism. This is the driving
force behind structural genomics projects, which can therefore be understood
as part of functional genomics. In particular for structures from these
large-scale efforts, interpretation is difficult since independent biological
experimental knowledge may be unavailable. Modelling techniques help in
identifying ligands and predicting the dynamics that is essential for the
function of the molecule. X-ray/electron crystal or NMR structures themselves
are only stills of the biologically active, dynamic molecules. Disregarding
some rare exceptions, there is no experimental technique that can observe
dynamics in atomic detail, and interpretation of spectroscopic
characterizations of dynamics is another important application of molecular
simulation. Even with structural genomics projects showing the first results,
the structure-sequence gap is widening at an increasing speed. Modelling is
therefore becoming a major source of structural information.
On the technical side, ever more powerful computers enable longer simulations
and consequently more meaningful results, and greater scope for direct
comparison with experiment. New experimental techniques (such as atomic force
spectroscopy and optical tweezers for studying single molecules) create new
needs for simulation. Further, advances in modelling and simulation
methodology are bringing improved accuracy and possibilities for new
applications.
Simulation techniques allow dynamic as well as structural features to be
explored. They permit computation of thermodynamic and kinetic properties.
They may be used to predict effects of mutations and changes in environmental
conditions such as pH. They are valuable in the design and redesign of new
molecules. Increasingly, therefore, non-specialists will find it necessary to
apply simulation techniques to biological macromolecules. The software has
become easier to obtain and often provides user-friendly graphical interfaces.
It is however essential to understand the basic principles underlying
different simulation techniques, and it is by no means easy for the novice
user to understand how to use powerful software to greatest advantage, and
results can be misinterpreted. The EMBO practical course will address three
types of simulation: quantum mechanics, molecular mechanics/dynamics and
Brownian dynamics. These permit simulation on different temporal and spatial
scales. They may be used as follows:
Quantum mechanics combined with molecular mechanics (in QM/MM calculations)
to investigate enzyme mechanisms and redox properties.
Molecular mechanics models with molecular dynamics or Monte Carlo simulations
to refine macromolecular structures, simulate dynamic motions and compute
thermodynamic and kinetic properties.
Brownian dynamics to simulate diffusional motion for molecular association
and conformational transitions.
One aim will be to provide the basic theory and practical hints for such users
e.g. biologists who want to simulate the molecule they are doing experiments
on. Another type of student will be doing theoretical research in a related
area e.g. homology modelling, or with one of the simulation techniques and
wish to learn how to expand their calculations to use (other) simulation
techniques.
At the end of the course, it is the intention that each student will have a
reasonable grasp of the theory behind each simulation method and know how to
put this into practice. Exercises will be done with software of minimal cost
so that users can continue once they get home. Assistance will be provided
with application of the methods to the students' own projects.
Tentative program
The course will start on Sunday 18th of July around 15h00 and
finish on Saturday 24th of July with dinner.
Force fields
Electrostatics
Molecular mechanics: energy minimization
Molecular dynamics
Monte Carlo techniques
Essential dynamics/ normal modes
Free energies
Brownian dynamics
Combining quantum mechanics and molecular mechanics approaches
Programming techniques
Molecular graphics
Modelling: some basics of mutations/sequence analysis
Docking/ drug design
Practicals will cover application of these techniques to enzyme mechanism,
protein and peptide folding, DNA/RNA binding and carbohydrate conformational
characterization.
Speakers and instructors:
Rebecca Wade, EML Heidelberg
Tom Simonson, Ecole Polytechnique, Palaiseau
Richard Lavery, IBPC, Paris
Konrad Hinsen, Centre de Biophysique Moleculaire, Orleans
Anna Tramontano, University of Rome
Warren DeLano, DeLano Scientific, San Francisco
David Case, Scripps Institute, La Jolla
Martin Field, IBS, Grenoble
Paolo Carloni, International School for Advanced Studies, Trieste
Michael Nilges, Pak-Lee Chau, Tru Huynh, Arnaud Blondel, Rachid Maroun, Institut Pasteur, Paris
Course fees and registration
NOTE: the course is very much overbooked. We were forced to
reject many good applications. All accepted participants have
been notified directly by email.
Please send an application by email (ascii preferred) to Michael Nilges, containing the following information:
(1) a short CV, with a list of publications (if possible);
(2) a letter of motivation indicating how the course will help you in your research;
(3) an abstract for a poster.
For participants from academic institutions, there are no course fees. All local expenses are paid by EMBO. Travel has to be paid by the participants.
The deadline for applications was 15th of May, 2004.
For more information, contact
Michael Nilges
or Rebecca Wade
NOTE: the course is very much overbooked. We were forced to
reject many good applications. All accepted participants have
been notified directly by email.
Course Materiel
Some course materiel is available:
Tom Simonson: Electrostatics
Konrad Hinsen: Normal modes
Konrad Hinsen: Programming
author: Michael Nilges
last change: June 1, 2004