Assignments for week 4

Protein Structure Modeling

Usefull Links For This Week

• Verify3D (profile method)
• Errat server
• Europeean Protein Verification server
• The course 96 list of links. This is the set of links that was found before the course.
• Added links during the course. If you find an interesting link please add it here.
• MBI at UCLA

Practical Reports

1. Try atleast two different protein verification servers the following proteins: 2pcy.pdb 434_1.pdb, st1.pdb, 1r69.pdb,and st2.pdb. These files can be found here. Are all these structures correct ? Please comment for each protein and all servers.


2. Try to make a homology model of the first sequence from the first assignment using the Swiss-modeller. Look at the model with RASMOL. Describe the difference between this file and the 1r69 pdb structure.

To understand before the reading seminars.

• Describe the different homology modelling methods decribed in the lectures ! Give some ideas why you think they are god or bad. What physical ideas are the basic of the different methods.
  Sali (Modeller)


• Abagyan (ICM)
  
• DeLarue (Mean Field Approach)
  
• What is the main difference between molecular dynamics and the ICM method.


• What are the major uses for molecular dynamics simulations ?.
• Describe the profile method. Advanteges disadvanteges ?
• Describe the errat method. Advanteges disadvanteges ?
• Describe the Sippl method for structure verification. Advanteges disadvanteges ?