FvFold: A model to predict antibody Fv structure using protein language model with residual network and Rosetta minimization.

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Abstract

The immune system depends on antibodies (Abs) to recognize and attach to a wide range of antigens, playing a pivotal role in immunity. The precise prediction of the variable fragment (Fv) region of antibodies is vital for the progress of therapeutic and commercial applications, particularly in the treatment of diseases such as cancer. Although deep learning models exist for accurate antibody structure prediction, challenges persist, particularly in modeling complementarity-determining regions (CDRs) and the overall antibody Fv structures. Introducing the FvFold model, a deep learning approach harnessing the capabilities of the ProtT5-XL-UniRef50 protein language model which is capable of predicting accurate antibody Fv structure. Through evaluations on various benchmarks, our model outperforms existing models, demonstrating superior accuracy by achieving lower Root Mean Square Deviation (RMSD) in almost all loops and Orientational Coordinate Distance (OCD) values in the RosettaAntibody benchmark, Therapeutic benchmark and IgFold benchmark compared to the previous top-performing model.Copyright © 2024. Published by Elsevier Ltd.