| Introductory Course on Molecular Simulations |
| |
| Monday 22 - Introduction |
| 09:00 |
Registration |
| 10:00 |
Opening S. Pantano L. Coitiño and O. Ventura
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| 10:15 |
O. Ventura Molecular Simulations in the South of the World |
| 11:20 |
A. Buschiazzo Introduction to Structural Biology: experimental methods their advantages and limitations
|
| 13:00-14:30 |
Lunch |
| 14:30 |
Local Organizers Structure Databases |
| 15:30 |
Coffee Break |
| 15:45 |
Local Organizers Brief Introduction to Linux |
| 18:00 |
Get-together party |
| 19:00 |
Shuttle departure to the Hotel
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| Tuesday 23 - Energy Calculations |
| 09:00 |
O. Ventura Hamiltonians |
| 10:00 |
S. Pantano Introduction to Molecular Mechanics |
| 11:00 |
Coffee Break |
| 11:15 |
L. Coitiño Hartree-Fock |
| 12:45 |
Felipe Trajtenberg (Uy) Structural insights on the thermosensor DesK from Bacillus subtilis |
| 13:00 |
Florencia Rey (Arg.) Structural and functional studies of Na-FAR-1 a novel fatty acid and retinol binding protein from Necator Americanus |
| 13:15 |
Rafael Caceres (Br) Crystal structure and molecular dynamics studies of human Purine Nucleoside Phosphorylase complexed with 7-deazaguanine |
| 13:30-14:30 |
Lunch |
| 14:30 |
Local Organizers Molecular Visualization I
|
| 15:30 |
Coffee Break |
| 16:00 |
Local Organizers Molecular Visualization II
|
| 18:00 |
Shuttle departure to the Hotel |
| |
|
| Wednesday 24 - DFT |
| 09:00 |
O. Ventura DFT |
| 10:00 |
O. Ventura Implementations |
| 11:00 |
Coffee Break |
| 11:15 |
L. Coitiño Solvation |
| 12:00 |
P. Saenz Reactivity |
| 12:45 |
Daniel Kurth (Arg) The essential carboxyltransferase accd6 as a target for novel anti-mycobacterial agents |
| 13:00 |
Horacio Poblete (Ch) Determination of binding free energy of selective inhibitors of human lipoxygenase 12 and 15 (hLOX) by molecular dynamics methods (FEP) |
| 13:15 |
Dardo Ferreiro (Arg) Dynamical changes upon activation of p38gamma |
| 13:30-14:30 |
Lunch |
| 14:30 |
Local Organizers Energy Minimization I
|
| 15:30 |
Coffee Break |
| 15:45 |
Local Organizers Energy Minimization II
|
| 18:00 |
Shuttle departure to the Hotel |
| |
|
| Thursday 25 - MD |
| 09:00 |
S. Pantano Molecular Dynamics I |
| 10:00 |
S. Pantano Molecular Dynamics II |
| 11:00 |
Coffee Break |
| 11:15 |
M. Segovia Introduction to Montecarlo |
| 12:15 |
Vanesa Galassi (Arg) Molecular dynamics of the interaction of an acidic soluble protein with anionic lipid |
| 12:30 |
Martin Dodes (Arg) Effects of lipids on the activity of Plasma Membrane Calcium Pump |
| 12:45 |
Ariela Vergara (Ch) Molecular dynamics and free energy perturbation analysis of Oseltamivir and Zanamivir binding to mutants of influenza virus (A/H1N1) |
| 13:00 |
Fernando Zamarreño (Arg) Interaction Fabp - Membrane: the electrostatic interactions could determine the choice of collisional or diffusional mechanism in fabps from different tissues |
| 13:15 |
Florencia Martini (Arg) Ca2+ adsorption to lipid membranes and the influence of the exposure of phosphate groups |
| 13:30-14:30 |
Lunch |
| 14:30 |
Local Organizers Molecular Dynamics I
|
| 15:30 |
Coffee Break |
| 15:45 |
Local Organizers Molecular Dynamics II
|
| 18:00 |
Shuttle departure to the Hotel |
| |
|
| Friday 26 - QM/MM |
| 09:00 |
S. Di Lella QM/MM I |
| 10:00 |
S. Di Lella QM/MM II |
| 11:00 |
Coffee Break |
| 11:30 |
S. Di Lella QM/MM III |
| 12:30 |
Marcos Madrid (Arg) Principal Component Analysis of Protein Structural Divergence |
| 12:45 |
Miguel Quiliano (Peru) Aryl piperazine and pyrrolidine as antimalarial agents. Synthesis, investigation of SAR and molecular modeling studies |
| 13:00 |
Ivani Pauli (Bra) Studies on the interactions of the enzyme InhA from Mycobacterium tuberculosis with small drug-like molecules |
| 13:15 |
Juan Pablo Bustamente (Arg) Structural and dynamical study of extreme conditions adapted hemeproteins using computer simulations techniques |
| 13:30-14:30 |
Lunch |
| 14:30 |
Local Organizers QM/MM I |
| 15:30 |
Coffee Break |
| 15:45 |
Local Organizers QM/MM II |
| 18:00 |
Shuttle departure to the Hotel |
| |
|
| Saturday 27 - Bioinformatics |
| 09:00 |
A. Turjanski Structural Bioinformatics |
| 11:00 |
Coffee Break |
| 11:15 |
D. Gonzalez Nilo Molecular Simulations of Transmembrane Proteins: K+ channels |
| 12:15 |
Laura Lafon (Uy) The cellular response to UV-C irradiation in nucleotide excision repair (NER) proficient or Cockayne syndrome B protein (CSB)-mutated Chinese hamster cell lines, is not affected by a poly-(ADP-ribose) (PAR) pool synthesized upon genotoxic stress |
| 12:30 |
Xaviera Lopez (Ch) In Silico study of decarboxylation of oxaloacetate in Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase |
| 12:45 |
Valeria Marquez (Ch) Role of the hydrophobic residues on the conductance of the potassium channel hSlo |
| 13:00 |
Aline Katz (Uy) Study of the movement of the WPD flexible loop of human protein tyrosine phosphatase PTP1B and the factors that influence it |
| 13:15 |
Humberto Gonzalez (Uy) Structural Microheterogeneity in capsular polysaccharides from Streptoccocus Pneumoniae
|
| 13:30-14:30 |
Lunch (Free Afternoon) |
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|
| Workshop on Computational Modelling and Simulation of Biological Systems |
| |
Monday 1 - Chairperson S. Pantano
|
| 09:00 |
P. Carloni Computational Molecular Medicine of HIV-1 |
| 10:00 |
M.A.C. Nascimento The construction of specific force fields for MD simulations |
| 10:40 |
O. Ventura Exploring the use of approximated methods to compute molecular properties by comparison with accurate methodologies for small systems |
| 11:20 |
Coffee Break |
| 11:40 |
Local Organizers QM/MM I |
| 13:15-14:30 |
Lunch |
| 14:30 |
Local Organizers QM/MM I |
| 15:30 |
Coffee Break |
| 15:45 |
Local Organizers QM/MM II |
| 18:30 |
Shuttle departure to the Hotel |
| |
|
Tuesday 2 - Chairperson L. Coitiño
|
| 09:00 |
O. Ventura Studying proteins using methods of electronic structure |
| 09:50 |
D. Estrin QM-MM applications to solvated species and enzymes |
| 10:40 |
M. Marti Computer simulation of biological membranes and related systems |
| 11:20 |
Coffee Break |
| 11:40 |
F. Herrera Structure and Dynamics of Raft-like systems |
| 12:20 |
M. Paulino Bioinformatics in Ligand-Based and Structure-Based Drug Design |
| 13:05 |
Tom Kelsey (Sco) The Casimir effect for inhomogeneous planar media |
| 13:30-14:30 |
Lunch |
| 14:30 |
F. Herrera Docking (Autodock) |
| 15:30 |
Coffee Break |
| 15:45 |
F. Herrera Docking (Autodock) |
| 18:30 |
Shuttle departure to the Hotel
|
| |
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Wednesday 3 - Chairperson D. Estrin
|
09:00
|
M. Delarue Simulation of the most probable transition pathway between two known forms of a macromolecule |
| 09:45 |
D. Estrin Simulation of chemical reactivity of heme proteins |
10:30
|
P. Dans Coarse Grain models of Nucleic acids at nearly atomistic resolution |
| 11:10 |
Coffee Break |
| 11:40 |
K. Coutinho Monte Carlo Method Applied in Simulations of Molecular Systems
|
| 13:30-14:30 |
Lunch |
| 14:30 |
K. Coutinho Solvation and Hydrogen bonds I
|
| 15:30 |
Coffee Break |
| 15:45 |
K. Coutinho Solvation and Hydrogen bonds II
|
| 18:30 |
Shuttle departure to the Hotel |
| |
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Thursday 4 - Chairperson O. Ventura
|
| 09:00 |
K. Coutinho Monte Carlo Simulations of Aggregations and Reactions in Solution and Use of S-QM/MM to Study Electronic Properties in Solution |
| 10:30 |
M. Skaf Interaction Between Drugs and Phospholipidic Monolayers and Biomembranes
|
| 11:20 |
Coffee Break |
| 11:40 |
M. Delarue Poisson-Boltzmann electrostatics: The dipolar solvent model |
| 12:10 |
S. Pantano A Coarse Grain Model for Bulk Water: WAT4? |
| 13:30-14:30 |
Lunch |
| 14:30 |
K. Coutinho Calculations of Relative Free Energy in Solution I |
| 15:30 |
Coffee Break |
| 15:45 |
K. Coutinho Calculations of Relative Free Energy in Solution II
|
| 18:30 |
Shuttle departure to the Hotel |
| |
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Friday 5 - Chairperson S. Pantano
|
| 09:00 |
P. Carloni Design of ligands with protein fibrillation in neurodegenerative diseases
|
09:45
|
M.A.C. Nascimento Protein folding: what can we learn from MD studies at high pressures?
|
| 10:30 |
M. Skaf Dynamics of Nuclear Receptors: Understanding the Behavior of Hormone Regulated Transcription Factors |
11:15
|
Coffee Break |
| 11:30 |
L. Coitiño Integrating modeling approaches in the study of DNA binding and bonding of transition metal anticancer drugs and probes
|
| 12:15 |
H. Naya (data driven?) Next generation biology |
| 13:00 |
Closing - Examination |
| 14:00 |
Lunch |
