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 PalaceThe 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

 

16:00-17:30

Registration

Miramar Palace

 

17:30-18:00

Welcome Speech

Miramar Palace

 

18:00-18:30

Martin Karplus Opening Speech

Miramar Palace

 

18:30

COCKTAIL

Miramar Palace

Monday26 September

Session 1

9:00-9:45

Introduction to Molecular Modeling and Empirical Energy Force Fields (Lennart Nilsson)

CFM

9:45-10:30

Topics in Advanced Force Field Development (Markus Meuwly)

CFM

 

10:30-11:00

Coffee Break

CFM

Session 2

11:00-11:45

Molecular Dynamics Simulations (Annick Dejaegere)

CFM

11:45-12:30

Normal Mode Analysis (Nathalie Reuter)

CFM

 

13:00-14:30

Lunch break

Olarain

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)

Barriola

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)

Barriola

Tuesday27 September

Session 3

9:00-9:45

Introduction to enhanced sampling molecular dynamics simulations I (Ferran Feixas)

CFM

9:45-10:30

Introduction to enhanced sampling molecular dynamics simulations II (Roland Stote)

CFM

 

10:30-11:00

Coffee Break

CFM

Session 4

11:00-11:45

A crash course in alchemical free energy simulations (Stefan Boresch and Ronen Zangi) Part I & Part II

CFM

11:45-12:30

Estimation of free energy along a reaction coordinate (Emanuele Paci)

CFM

 

13:00-14:30

Lunch break

Olarain

Practical 3

15:00-16:30

Enhanced sampling molecular dynamics simulations (Ferran Feixas and Roland Stote)

Barriola

Practical 4

16:30-18:00

Alchemical free energy simulations (Stefan Boresch, Emanuele Paci, Ronen Zangi)

Barriola

Wednesday28 September

Session 5

9:00-10:00

Homology Modeling (Leif A. Eriksson)

CFM

10:00-11:00

Translational Medicine: From Theory to the Patient Bedside (O. Michielin)

CFM

 

11:00-11:20

Coffee Break

CFM

Session 6

11:30-12:30

Ligand-based virtual screening (V. Zoete and A. Daina)

Barriola

 

13:00-14:30

Lunch break

Olarain

Practical 5

15:00-15:55

Reverse screening and target prediction(V. Zoete and A. Daina)

Barriola

15:55-16:50

Fragment-based ligand design(V. Zoete and A. Daina)

Barriola

 

16:50-17:10

Break

Barriola

Practical 6

17:10-18:05

Absorption Distribution Metabolism Excretion Toxicity (ADMET)(V. Zoete and A. Daina)

Barriola

18:05-19:00

Docking using Autodock Vina within UCSF Chimera Docking(Leif A. Eriksson)

Barriola

Thursday29 September

 

9:00-11:00

Poster Session

Santamaria

 

11:00-17:30

Free time

 

 

17:30-20:30

Passion For Knowledge

Victoria Eugenia Theatre

Friday30 September

Session 7

9:00-9:45

Continuum electrostatics: from solving boundary value problems to membrane permeability of peptides (Michael Schaefer)

CFM

9:45-10:30

Introduction to Multiscale Quantum Mechanical/Molecular Mechanical calculations (Pedro A. Fernandes)

CFM

 

10:30-11:00

Coffee Break

CFM

Session 8

11:00-11:45

QM/MM study of a reaction mechanism: the case of Carboxypeptidase A (Joni Mujika)

CFM

11:45-12:30

Tying it all together: a holistic approach to study mechanisms of catalysis with theory and experiment (Darrin M. York) 

CFM

12:30-12:40

Concluding Remarks (Emanuele Paci)

CFM

 

12:40-14:00

What Does the Future Hold (Martin Karplus)

CFM

 

14:00-15:00

Lunch break

Olarain

Practical 7

15:30-16:30

Practical on continuum Electrostatics. (Michael Schaefer) (Tar file with exercises)

Barriola

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)

Barriola

21:30

21:30

Dinner at the Cofradia Vasca de Gastronomia  (Old part of the city)

 

Campus Map:

 

 

  Download the material of the practicals here