Tools
PLACER
Rank protein-ligand conformations
PLACER performs local docking for a protein/small molecule complex to sample conformations. It accurately generates structures of organic small molecules bound to active sites, and can generate conformations of structures of small molecules and protein side chains. PLACER enables generation of ensembles of solutions to model conformational heterogeneity.
PLACER can be used to assess accuracy of designed active sites for increased enzyme activity.
Experimental Validation
Used to design a retroaldolase with a kcat/KM of 11000 M-1min-1 - higher than any pre-deep learning design for this reaction.
Used in Serine Hydrolase design pipeline (reach out if you’re interested in this protocol)