OptCDR is used in the de novo design of antibody binding pockets against specified antigen epitopes. This is done in a four-step procedure. First, canonical structures are selected for the six complementarity determining regions (CDRs). Next, the amino acid sequences of the selected structures are initialized. This is followed by several thousand iterations of our IPRO procedure to refine the backbones and amino acids of the CDRs. Finally, accumulating the most promising mutations generates a library of antibodies.
Pantazes, R.J. and C.D. Maranas (2010), "OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding," Protein Engineering, Design & Selection, 23(11): 849-58.
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