Program
Location
Mathematics Lecture Room 2 (G19)
Handouts
Hands-on Sessions (pdf)
Mac Primer (html)
Unix Primer (html)
Week
1
Mon, 6/7: Introduction to Protein
Structure and
Dynamics
09:00-09:30 |
Opening Remarks (pdf) |
09:30-11:00 |
Molecular Graphics Perspective of
Protein Structure
and
Function (pdf)
|
Coffee Break |
|
11:30-12:30 |
Molecular Dynamics Method (pdf,
pdf) |
12:30-12:45 |
Daily Q & A |
Lunch Break |
|
14:00-14:45 |
Overview of Hands-on Sessions (E.
Villa, F.
Khalili) |
15:00-18:00 |
Molecular Graphics Tutorial (pdf)
(E. Villa, F. Khalili, R. Amaro) |
Tue, 6/8: Introduction to
Bioinformatics
09:00-10:00 |
Sequence structure and alignment (pdf) |
10:00-11:00 |
Evolution of Protein Structure (pdf) |
Coffee Break |
|
11:30-12:30 |
Bioinformatics of tRNA Synthase (pdf) |
12:30-12:45 |
Daily Q & A |
Lunch Break |
|
14:30-16:00 |
Sequence Alignment Algorithms (pdf)
(R.Amaro, E. Villa, F. Khalili) |
16:00-18:00 |
Evolution of tRNA Synthetases (pdf)
(R.Amaro, E. Villa, F. Khalili) |
Wed, 6/9: Statistical Mechanics of
Proteins
09:00-10:00 |
Equilibrium Properties of Proteins (pdf,
pdf) |
10:00-11:00 |
Nonequilibrium Properties of
Proteins(pdf) |
Coffee Break |
|
11:30-12:30 |
Simulated Cooling of Proteins (pdf,
pdf) |
12:30-12:45 |
Daily Q & A |
Lunch Break |
|
14:00-18:00 |
Molecular Dynamics Tutorial (pdf)
(E.
Villa, F. Khalili, R. Amaro) |
Thu, 6/10: Steered Molecular Dynamics
of Proteins
09:00-10:00 |
Introduction and Examples (pdf) |
10:00-11:00 |
Mechanical Proteins (pdf) |
Coffee Break |
|
11:30-12:30 |
Determining Potentials (pdf) |
12:30-12:45 |
Daily Q & A |
Lunch Break |
|
14:00-18:80 |
Molecular Dynamics Tutorial (pdf)
(E. Villa, F. Khalili, R. Amaro)
|
Fri, 6/11: Modeling Large Systems
09:00-10:00 |
Molecular Machines of the Living Cell
(pdf) |
10:00-11:00 |
Light Harvesting in Photosynthesis (pdf) |
Coffee Break |
|
11:30-12:30 |
ATP Synthase (pdf) |
12:30-12:45 |
Daily Q & A |
Lunch Break |
|
14:30-15:30 |
Stretching Deca-Alanine (pdf)
(E. Villa, F. Khalili, R. Amaro) |
Week
2
Mon, 6/14: Introduction to Protein
Structure and Protein
Bioinformatics
|
New
Participants |
09:00-10:00 |
Molecular Graphics Perspective of
Protein Structure and
Function
(pdf,
pdf)
|
10:00-11:00 |
Introduction to Bioinformatics (pdf,
pdf
) |
Coffee Break |
|
11:30-12:30 |
Evolutionary analysis of aquaporins (pdf)
|
|
|
|
Continuing Participants
(IAS Conference Room)
|
9:00-12:00
|
Model your own system with assistance
from teaching
assistants (E. Villa, F. Khalili, R. Amaro)
|
|
|
12:30-12:45
|
Daily Q&A
|
Lunch
Break |
|
|
New
Participants |
14:00-14:30
|
Overview
of Hands-on
Sessions (E. Villa, F.
Khalili, R. Amaro) |
14:30-16:30
|
Molecular
Graphics
Tutorial (pdf)
(E. Villa, F. Khalili) |
16:30-18:00
|
Bioinformatics
of
Aquaporins (pdf)
(E. Villa, F. Khalili) |
|
|
|
Continuing Participants
|
14:00-18:00
|
Model
your own system
|
|
|
Tue, 6/15: Introduction
to Protein Dynamics
|
New
Participants |
09:00-10:00 |
Equilibrium Properties of the
Proteins (pdf,
pdf)
|
10:00-11:00 |
Non-equilibrium Properties of
the Proteins (pdf) |
Coffee Break |
|
11:30-12:30 |
Simulated Cooling of the Proteins (pdf,
pdf)
|
|
|
|
Continuing Participants
(IAS Conference Room)
|
9:00-12:00
|
Model your own system with assistance
from teaching
assistants (E. Villa, F. Khalili, R. Amaro)
|
|
|
12:30-12:45
|
Daily Q&A
|
Lunch
Break |
|
|
New
Participants |
14:00-18:00
|
Molecular
Dynamics
Tutorial (pdf)
(E. Villa, F. Khalili, R. Amaro) |
|
|
|
Continuing Participants |
14:00-18:00
|
Model
your own system with
the assistance from teaching assistants (E. Villa, F. Khalili, R. Amaro)
|
Wed, 6/16: Parameters for Classical
Force Fields
09:00-10:00 |
Introduction and Examples (pdf)
|
10:00-11:00 |
Introduction to Classical Force
Fields (pdf)
|
Coffee Break |
|
11:30-12:30 |
Methods of Parametrization (pdf)
|
12:30-12:45 |
Daily Q&A
|
Lunch Break |
|
14:30-15:30 |
System set-up of HisH with the
Molecular Modeling
package MOE* (pdf)
(R. Amaro, E. Villa, F. Khalili)
|
15:30-18:00 |
Semiempirical Parameter Gerneration
with Spartan (R.
Amaro, E. Villa, F. Khalili) (pdf)
|
Thu, 6/17: Simulating Membrane
Channels
09:00-10:00 |
Introduction and Examples (pdf)
|
10:00-11:00 |
Transport in Aquaporins (pdf)
|
Coffee Break |
|
11:30-12:30 |
Nanotubes (pdf)
|
12:30-12:15 |
Daily Q&A
|
12:15-12:45 |
Concluding Remarks
|
Lunch Break |
|
14:00-15:00 |
Bioinformatics of Aquaporins (pdf)
(E. Villa, F. Khalili, R. Amaro) |
15:00-18:00 |
Nanotubes (pdf)
(E. Villa, F. Khalili, R. Amaro) |
Fri, 6/18: Participants
Presentations
09:00-10:30 |
Participants Presentations (pdf)
|
Coffee Break |
|
12:10 |
Summary of the Workshop (Klaus
Schulten)
|
|