Program
The inauguration of the course will consist of an opening speech by Nobel Laureate Prof. Martin Karplus, and a welcome-reception coktail at the Miramar Palace. The core of the course will consist of morning lectures, a set of related afternoon practicals (see the complete program below), and a seminar by Martin Karplus. The participants will be also invited to attend the seminar at the Passion for Knowledge symposium at the Victoria Eugenia Theatre. Download the programe here.
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Sunday25 September |
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16:00-17:30 |
Registration |
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17:30-18:00 |
Welcome Speech |
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18:00-18:30 |
Martin Karplus Opening Speech |
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18:30 |
COCKTAIL |
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Monday26 September |
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9:00-9:45 |
Introduction to Molecular Modeling and Empirical Energy Force Fields (Lennart Nilsson) |
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9:45-10:30 |
Topics in Advanced Force Field Development (Markus Meuwly) |
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10:30-11:00 |
Coffee Break |
CFM |
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Session 2 |
11:00-11:45 |
Molecular Dynamics Simulations (Annick Dejaegere) |
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11:45-12:30 |
Normal Mode Analysis (Nathalie Reuter) |
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13:00-14:30 |
Lunch break |
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Practical 1 |
15:00-16:30 |
From Parameters to Dynamics I: Parameter generation for novel ligands and Advanced Force Fields (L. Nilsson, M. Meuwly, A. Dejaegere and N. Reuter) |
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Practical 2 |
16:30-18:00 |
From Parameters to Dynamics II: Molecular Dynamics Simulations and Normal Mode Analysis of a Protein-Ligand Complex (L. Nilsson, M. Meuwly, A. Dejaegere and N. Reuter) |
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Tuesday27 September |
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Session 3 |
9:00-9:45 |
Introduction to enhanced sampling molecular dynamics simulations I (Ferran Feixas) |
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9:45-10:30 |
Introduction to enhanced sampling molecular dynamics simulations II (Roland Stote) |
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10:30-11:00 |
Coffee Break |
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Session 4 |
11:00-11:45 |
A crash course in alchemical free energy simulations (Stefan Boresch and Ronen Zangi) Part I & Part II |
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11:45-12:30 |
Estimation of free energy along a reaction coordinate (Emanuele Paci) |
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13:00-14:30 |
Lunch break |
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Practical 3 |
15:00-16:30 |
Enhanced sampling molecular dynamics simulations (Ferran Feixas and Roland Stote) |
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16:30-18:00 |
Alchemical free energy simulations (Stefan Boresch, Emanuele Paci, Ronen Zangi) |
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Wednesday28 September |
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Session 5 |
9:00-10:00 |
Homology Modeling (Leif A. Eriksson) |
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10:00-11:00 |
Translational Medicine: From Theory to the Patient Bedside (O. Michielin) |
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11:00-11:20 |
Coffee Break |
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Session 6 |
11:30-12:30 |
Ligand-based virtual screening (V. Zoete and A. Daina) |
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13:00-14:30 |
Lunch break |
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Practical 5 |
15:00-15:55 |
Reverse screening and target prediction(V. Zoete and A. Daina) |
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15:55-16:50 |
Fragment-based ligand design(V. Zoete and A. Daina) |
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16:50-17:10 |
Break |
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Practical 6 |
17:10-18:05 |
Absorption Distribution Metabolism Excretion Toxicity (ADMET)(V. Zoete and A. Daina) |
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18:05-19:00 |
Docking using Autodock Vina within UCSF Chimera Docking(Leif A. Eriksson) |
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Thursday29 September |
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9:00-11:00 |
Poster Session |
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11:00-17:30 |
Free time |
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17:30-20:30 |
Passion For Knowledge |
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Friday30 September |
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Session 7 |
9:00-9:45 |
Continuum electrostatics: from solving boundary value problems to membrane permeability of peptides (Michael Schaefer) |
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9:45-10:30 |
Introduction to Multiscale Quantum Mechanical/Molecular Mechanical calculations (Pedro A. Fernandes) |
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10:30-11:00 |
Coffee Break |
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Session 8 |
11:00-11:45 |
QM/MM study of a reaction mechanism: the case of Carboxypeptidase A (Joni Mujika) |
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11:45-12:30 |
Tying it all together: a holistic approach to study mechanisms of catalysis with theory and experiment (Darrin M. York) |
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12:30-12:40 |
Concluding Remarks (Emanuele Paci) |
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12:40-14:00 |
What Does the Future Hold (Martin Karplus) |
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14:00-15:00 |
Lunch break |
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Practical 7 |
15:30-16:30 |
Practical on continuum Electrostatics. (Michael Schaefer) (Tar file with exercises) |
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Practical 8 |
16:30-18:30 |
Hands-On Workshop on the Reaction Mechanism of Carboxypeptidase A (Pedro A. Fernandes, Jon I. Mujika and Darrin M. York) |
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21:30 |
21:30 |
Dinner at the Cofradia Vasca de Gastronomia (Old part of the city) |
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Download the material of the practicals here