Structure Prediction Applications

Ab initio protein folding performs task of predicting 3-D structural models for a protein molecule from its sequence information. The simulation is done in low-resolution mode. Then the resulting models are clustered and the cluster centers are subjected to full-atom structure refinement.

AbinitioRelax is the combination of ab initio folding and refinement by relax. Previously, the standard protocol for structure prediciton task was to fold the protein de novo, cluster low-energy models, select cluster centers for further "relax" refinement. The advantage of this protocol is that it is relatively time efficient since ab initio folding is faster and relax is more time-consuming. However, the potential drawback is that if no near-native models are populated after ab initio folding, it is impossible to correct them during the refinement stage. With more and more computational power available, the "abrelax" protocol is created to streamline this process by doing ab initio folding followed directly by "relax". Obviously, this protocol is much more time-demanding and show improvement only when enough sampling is paid (partially due to the fact that fullatom energy function is very sensitive to imperfect atomic interactions and more noise will be introduced if the task is performed only with insufficient sampling.

Applications

We have an application ready at src/apps/public/AbinitioRelax.ccm, it perofrms classic Abinitio and AbRelax simulations. You can find the executables of abinitio application in mini/bin/ after successfully compiling.

We will briefly introduce the AbinitioRelax application in this page. You can find the details boinc docs from Boinc Section.

Command Lines and Options

• Sample Command Line: AbinitioRelax.linuxgccrelease .silent > folding.log
• Options used in AbinitioRelax application:

  -database                  Path to rosetta3 databases. [PathVector]
  -abinitio:relax            Do a relax after abinitio = abrelax, default=false. [Boolean]
  -in:file:native            Native PDB filename. [File]
  -in:file:frag3             Fragments file with residue length of 3 [String]
  -in:file:frag9             Fragments file with residue length of 9 [String]
  -out:nstruct               Number of times to process each input PDB. [Integer]
  -out:file:silent           Use silent file output, use filename after this flag. [FileVector]
  

Result Interpretation

There are two kinds of output files generated during this abinitio run. One is the pdb file, the other is energy fasc(fullatom scoring) file.

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