SPDesign is a method for protein sequence design based on structural sequence profile using ultrafast shape recognition. Given an input backbone structure, SPDesign utilizes ultrafast shape recognition vectors to accelerate the search for similar protein structures in our in-house PAcluster80 structure database, and then extracts the sequence profile through structure alignment. Combined with structural pre-trained knowledge and geometric features, they are further fed into an enhanced graph neural network for sequence prediction. Experimental results show that SPDesign significantly outperforms the state-of-the-art methods. Notice: During the CASP season (04/23/2024-09/01-2024), SPDesign sever will be out of service.

• 2023/09/20: SPDesign version 1.0 is released.

• Hui Wang^✝,Dong Liu^✝,Kailong Zhao, Yajun Wang* and Guijun Zhang*. SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition. Briefings in Bioinformatics, 2024, 25(3): bbae146, DOI: 10.1093/bib/bbae146.