[ fp | protdockgrid | dps | hm ]

 
 plotBestEnergy "f1" 100. "append display" 

 
# peptide "pep.se" ; runs: "f1" and "f2" 
  build "pep" 
  display 
  read conf "f1" 0 
  show stack 
  read conf "f2" 0 
  show stack 

 
                     # 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 movie     # run it and record a movie.  
                      # watch the movie later by:  
                      # read movie "f2"; display ribbon 
                      # display movie "f2" 4. 8. 
                      # analyze the best conf. in the stack by: 
                      # build "pep16"; read stack; show stack all 
                      # load conf 1 
 quit 

1. Creating two ICM objects for both proteins with the convertObject macro
2. Specify project parameters in a special table
3. Orient molecules, choose the docking box and make potentials.
4. Dock the protein ligand into the potentials.
5. Refine the solutions.

1. Create ICM-objects of the two proteins you want to dock.
2. Use macro makeSimpleDockObj to create two simplified objects.
3. Combine two simplified objects into one and prepare it for docking simulation using _makeComplex script. During the execution you will be prompted for orientation of the first molecule, which should face the second one with the expected epitope.
4. Run the docking simulation using _dock2mol script. To insure the completeness of the search, run 3-4 simulations in parallel and compare the resulting stacks, the top 5-7 conformations should be the same except for 1-2. Combine the stacks using "read stack append" command with subsequent filtering by

    
    vicinity = 4. 
    compare static a_2//ca 
    compress stack 
   

5. Prepare .var files with optimized surface sidechain conformations for individual proteins by running _surfSideChainOpt script.
6. Run _makeFullAtom script to create full atom models from the simplified conformations accumulated in the stack.
7. Run _refineComplex script on each of the full atom models
8. Complex with the best energy after the optimization is (hopefully) the answer.

• homodel macro: fast interactive model building.
• _homFast for fast model building (substitute nonidentical side-chains, assign the most likely rotamer).
• _hom for more rigorous model building for one polypeptide chain: side-chains are optimally placed loops are automatically recognized and simulated.
• _homMult the same as the above script, but for a multichain protein molecule, e.g. an immunoglobulin molecule. Requires a set of separate files for each alignment.