[Dock-fans] amber score structures

Scott Brozell sbrozell at rci.rutgers.edu
Thu Jun 2 19:30:04 PDT 2016


Hi,

On Thu, Jun 02, 2016 at 01:33:33PM +0000, barbara rossi wrote:
> I performed amber score on a protein-ligand complex by allowing flexibility on the receptor structure
> 
> All is fine BUT I do not understand why the structure of the protein in protein.ligand.final_pose.pdb is slightly different from those in protein.final_pose.pdb.
> 
> Aren't both structures referring to the optimized complex?

The short answers are no and that the slightly different structures
represent the induced fit:
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/amber_score/amber_score.htm

In more detail
amber_score_receptor_file_prefix.final_pose.amber.pdb
contains the protein structure after the Amber score protocol is
applied to the protein only; this structure is the same for all ligands.

amber_score_receptor_file_prefix.AMBER_SCORE_ID.final_pose.amber.pdb
contains the protein-ligand complex structure after the Amber score
protocol is applied to the protein-ligand complex in which the
protein part is movable according to your first sentence; this complex
structure likely differs in the protein part across all ligands.

For more on the protocol see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreEnergy

For more on the outputs see
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreOutputs

scott



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