GalaxyCSAlign(-Dock)

Method for GalaxyCSAlign(-Dock)

CSAlign

CSAlign predicts 3D structure of query ligand structure aligned to reference ligand structure

CSAlign-Dock

CSAlign-Dock predicts protein-ligand complex structure using information of given reference complex structure




Inputs for GalaxyCSAlign(-Dock)

User Information

First, you have to enter the following information required for modeling.
  • Job name: Enter job name for your recognition.
  • E-mail address: GalaxyWEB server will send progress reports of your job.

Assigning run type: CSAlign or CSAlign-Dock

You have to select between two methods
CSAlign: Structure alignment of query ligand to reference ligand
CSAlign-Dock: Alignment-based protein-ligand docking

Inputs

For both CSAlign and CSAlign-Dock,
you have to provide information on query ligand in smiles or in 3D structure in format of MOL2, PDB or XYZ.

For CSAlign,
you have to provide 3D structure of reference ligand in MOL2, PDB or XYZ format.
For CSAlign-Dock,
you have to provide 3D structure of reference complex structure in PDB format.



Outputs for GalaxyCSAlign(-Dock)

Predicted Structures

Top 5 ligand or protein-ligand complex models are shown.

Information and Download

For each model structures, combined scores and alignment scores are provided
along with the binding site interaction data.

Users can download all 50 structures generated by CSAlign or CSAlign-Dock.
Among downloaded files, out_fb.mol2 contains 50 predicted binding poses in MOL2 format, and
out_fb.E.info contains information on their scores.



References for GalaxyCSAlign(-Dock)