GeoAB: Towards Realistic Antibody Design and Reliable Affinity Maturation
LIN, H.; Wu, L.; Yufei, H.; Liu, Y.; Zhang, O.; Zhou, Y.; Sun, R.; Li, S. Z.
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Increasing works for antibody design are emerging to generate sequences and structures in Complementarity Determining Regions (CDRs), but problems still exist. We focus on two of them: (i) authenticity of the generated structure and (ii) rationality of the affinity maturation, and propose GEOAB as a solution. In specific, GeoABDesigner generates CDR structures with realistic internal geometries, composed of a generative geometry initializer (Geo-Initializer) and a position refiner (Geo-Refiner); GeoAB-Optimizer achieves affinity maturation by accurately predicting both the mutation effects and structures of mutant antibodies with the same network architecture as Geo-Refiner. Experiments show that GEOAB achieves state-of-the-art performance in CDR co-design and mutation effect predictions, and fulfills the discussed tasks effectively.
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