Abstract: A Method of generating binding peptide sequences to a target sequence, the method comprising: Receiving, using a processor configured by code executing therein, a data object corresponding to a protein target; Searching, using the data object, a protein interaction database for at least one partner protein to the target protein; Identifying at least one partner protein to the target protein; Providing the at least one partner protein to a computational model configured to output a predicted protein sequence predicted to interact with the target sequence; and Identifying at least one subsequence within the predicted protein sequence that meets a predetermined interaction threshold.

Abstract: A system and method of using contrastive language-image pre-training (CLIP) to devise a unified, sequence-based framework to design target-specific peptides via contrastive learning. In one or more further implementations, using known experimental binding proteins as scaffolds, a method is provided to generate a streamlined inference pipeline that efficiently selects peptides for downstream screening. In a further implementation, one or more compounds that are fused candidate peptides to E3 ubiquitin ligase domains that exhibit robust intracellular degradation of pathogenic protein targets in human cells.

Abstract: An isolated chimeric molecule is provided comprising: (i) a degradation domain comprising an E3 ubiquitin ligase motif without lysine residues; (ii) a targeting domain comprising a substrate-binding motif which is heterologous to the E3 ubiquitin ligase motif and configured to bind to Beta-Catenin; and (iii) a linker coupling said degradation domain to said targeting domain.