Patent ID: 11869629
Assignee: PYTHIA LABS, INC.
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 15:
16. A system for in silico design of a custom biologic structure for binding to a target via an artificial intelligence (AI)-powered interface designer module, the system comprising:
a processor of a computing device; and
a memory having instructions stored thereon, wherein the instructions, when executed by the processor, cause the processor to:
(a) receive and/or generate a scaffold-target complex model that represents at least a portion of a complex comprising the target and a particular candidate peptide backbone on which to build a custom interface portion of a ligand for binding to the target, wherein the particular candidate peptide backbone is oriented at a particular pose with respect to the target and the scaffold-target complex model comprises a representation of (i) at least a portion of the target and (ii) at least a portion of the candidate peptide backbone, said portions of the target and candidate peptide backbone located in proximity to each other and forming a potential binding interface;
(b) generate, based on the scaffold-target complex model, one or more prospective ligand-target complex models, each representing at least a portion of a complex comprising the target and a particular prospective ligand, each particular prospective ligand: (i) having a peptide backbone corresponding to the particular candidate peptide backbone, (ii) positioned with respect to the target based on the particular pose, and (iii) comprising at least an interface region, located in proximity to the target, populated with amino acids, such that each particular prospective ligand comprises a particular amino acid population at its interface region;
(c) for each of the one or more prospective ligand-target complex models, determine an interface score using a machine learning model, thereby determining one or more interface scores;
(d) select a subset of the prospective ligand-target complex models based on at least a portion of the one or more interface scores; and
(e) provide the selected subset of prospective ligand-target complex models for use in designing the custom biologic structure for binding to the target.