|Rosetta 3.1 Release Manual|
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.
We will briefly introduce the AbinitioRelax application in this page.
-database Path to Rosetta 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, default=default.out [String] -out:pdb Use PDB file output, default=false [Boolean] -out:path Path where PDB output files will be written to, default '.' [Path]