TCB Hands-on Workshop in Perth

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)


* MOE licenses available via an agreement with CGG