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.
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 |
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