Anti Body Builder 3 (ABB3)

Overview

ABB3 is an antibody structure prediction model. It is important to predict the structure so that biophysical properties of proteins can be predicted.

Inputs

• Heavy and light chain variable sequence

• PDB file name to save the predicted antibody structure

• To force ABB3 to run even if the sequence is invalid (true) or not (false) - default false

Outputs

• New antibody structure displayed in 3D Viewer

• PDB file containing antibody structure predicted by ABB3

Description

(https://academic.oup.com/bioinformatics/article/40/10/btae576/7810444)

ABB3 is a structure prediction model. EMLy passes the inputs given to an API endpoint called Antibody Builder 3 Endpoint which predicts the antibody structure. ABB3 models CDR loops by leveraging large language model embeddings. Frame Aligned Point Error is used to train the model. During training, the SAbDab is used to train the antibodies, and the IGMT system is used for renumbering.