This is a resumed protocol for running the Ab initio program from Rosetta Suite.
There are 3 files that you require to run the Ab initio protocol:
- Your sequence to be modeled
- Fragment 03
- Fragment 09
"Fragment Libraries are the pieces of experimentally
determined structures that Rosetta uses to guide the search of
conformational space when predicting structures using the Ab initio
protocol."
I recommend to use the Robetta Server to build your fragment libraries here. Then you will have the option to download the files, and also to download secondary structure information in a ss2 file. This will be helpful to the construction of your model.
The next step is to get into the Ab initio program. You will need to call the program with the full path i.e. /usr/local/rosetta3.5/bin/AbinitioRelax.default.linuxgccrelease. Then you need to run your program with the following flags:
-in:file:fasta your_seq.fasta
-in:file:frag3 /PATH/TO/FRAG3_FILE
-in:file:frag9 /PATH/TO/FRAG9_FILE
-database /PATH/TO/rosetta_database
-abinitio:relax
-relax:fast
-psipred_ss2 t000_.psipred_ss2.txt
-out:pdb -abinitio::increase_cycles 10
-abinitio::rg_reweight 0.5
-abinitio::rsd_wt_helix 0.5
-abinitio::rsd_wt_loop 0.5
-out:file:silent name_silent.out
-nstruct X
The number in nstruct flag will depend in the amount of structures you want to generate.
This Ab initio protocol performs in a good manner for small monomeric proteins in the range of 100 or less residues. For larger protein you will need to generated a nstruct in the range of 6,000 to 20,000 models, which need higher computing to encompass a larger conformational space.
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| Example of the result from an Ab initio protocol. The protein correspond to the B20 antibody, showing in yellow the model of the variable region. |
The following references provide information relevant to the sampling problem:
- Bradley P, Misura KM, Baker D (2005). Toward high-resolution de novo structure prediction for small proteins. Science 309, 1868-71.
- Kim DE, Blum B, Bradley P, Baker D (2009). Sampling bottlenecks in de novo protein structure prediction. J Mol Biol 393, 249-60.
More info in the Rosetta Commons Documentation.
