Three motifs to get going on modeling 1f1t, including ROS.params to model tetramehylrhodamine ligand:
-[x] Easiest loop MG_TMR_Uturn (solvable) is four-nucleotide U-turn containing loop – here's an overlay
-[x] Another MG_TMR_Aflap is a loop + bulge (4nts) total
-[x] Most ambitious is to seed with central C-G base pairs that intercalate ligand, and build rest from scratch. Not solvable yet, but stepwise appears to run fine.
-[ ] Need to create a puzzle that actually models intercalation of the ligand into the central CG/CG base pair step – would need to define stacking for arbitrary ligands in stepwise BaseCentroidScreener, or some kind of pre-docking and specification of submotifs. Would be a fun starter project!
Three motifs to get going on modeling 1f1t, including ROS.params to model tetramehylrhodamine ligand:
-[x] Easiest loop
MG_TMR_Uturn(solvable) is four-nucleotide U-turn containing loop – here's an overlay -[x] AnotherMG_TMR_Aflapis a loop + bulge (4nts) total -[x] Most ambitious is to seed with central C-G base pairs that intercalate ligand, and build rest from scratch. Not solvable yet, butstepwiseappears to run fine. -[ ] Need to create a puzzle that actually models intercalation of the ligand into the central CG/CG base pair step – would need to define stacking for arbitrary ligands in stepwiseBaseCentroidScreener, or some kind of pre-docking and specification of submotifs. Would be a fun starter project!