GalaxyAbDesign-H3Loop

GNN-based modeling of antibody H3 loop backbone atoms

Method for GalaxyAbDesign-H3Loop

GalaxyAbDesign-H3Loop is a method to predict the coordinates of antibody H3 loop backbone atoms from their local environment by a GNN-based inference procedure.

Inputs for GalaxyAbDesign-H3Loop

The following information is required:

  • Job name: Enter job name for your recognition.
  • E-mail address: GalaxyWEB server will send progress reports of your job (if provided).
  • PDB file: Prepare Chothia-numbered antibody Fv model PDB files. The IDs for the heavy and light chains must be H and L, respectively. The PDB files must contain lines for the backbone atoms of the H3 residues. Coordinates for the H3 residues are not used and need not be correct.

Outputs for GalaxyAbDesign-H3Loop

The method will output 16 model structures in PDB format. Only backbone atoms for the H3 loop are generated. Returned model structures are not physically correct (i.e., wrong bond distances and angles) and should be refined before further use.

Download

The generated structures could be downloaded.