[ tut3g ]

Objective

To superimpose two structures.

Background

In this lesson we demonstrate the use of a superposition based upon a sequence alignment. All superposition analyzes can be performed using the button available within the Analyses tab. The example here uses protein kinase structures to superimpose.

Instructions

1. File/Open/Example_Alignment.icb
2. Read PDB 2PHK
3. Extract the sequence from 2PHK and then drag it and drop it into the alignment.
4. Select a region of the alignment around which you wish to superimpose. You can use the propogate to all sequences in the Alignment Editor to make this selection.
5. Select the display tab and click on the superimpose button.

Notes and Things To Try:

• Try making a superposition around the ligand binding pocket only by selecting the ligand.
• Try improving poorly superimposed regions such as loops.

Manual References (Web Links)

How to Superimpose Two Structures

h2- Protein Folding and Structure Prediction {Folding}

Objective

To use a script to perform protein folding / structure prediction.

Instructions

                     # Example folding script. Use as directed. 
 read libraries 
 build "pep16"       # your peptide sequence is in pep16.se file. 
 rename a_*. "f2"    # specifies current name.  
                     # Several runs (f2,f3, etc.) are recommended 
 nvar = Nof( v_//* ) # number of variables 
 
 nProc=4             # if you are using parallel version.  
 
 mncallsMC    = nvar*50000  # maximal number of energy evaluations 
 mncalls      = 170+nvar*3  # maximal n_of minimization calls after 
                            # each random change 
 temperature  = 600   # optimal temperature for the simulation 
 tolGrad      = 0.01  # exit minimization when gradient is < 0.01 
 mcBell       = 1.0   # the default width of the MC probability distributions 
 mnconf       = 40    # maximal n_of low-energy conformations saved  
                      # in the stack (f2.cnf file) 
 mnvisits     = 25    # if stuck for >= 25 times, push it out 
 mnreject     = 10     
 mnhighEnergy = 30     
 l_bpmc       = yes   # use biased probability  
 electroMethod = "MIMEL" 
 surfaceMethod = "constant tension" 
 set terms "vw,14,hb,el,to,sf,en" 
                      # ECEPP/2 energy + solvation + entropy (see icm.hdt file) 
 
 fix v_//?vt*         # exclude irrelevant virtual variables specifying  
                      # absolute molecular position 
 set vrestraint a_/*  # load preferred backbone and side-chain angle zones 
                      # for the  biased probability MC 
 randomize v_//!omg 180.0  # create random starting conformation 
 vicinity = 15.0       
 compare v_//phi,psi  # use these variables to compare structure 
 montecarlo trajectory # run it and record a trajectory file.  
                      # watch the movie later by:  
                      # read trajectory "f2"; display ribbon 
                      # display trajectory "f2" 4. 8. 
                      # analyze the best conf. in the stack by: 
                      # build "pep16"; read stack; show stack all 
                      # load conf 1 
 quit