The present invention provides a structure-based methodology for efficiently generating and screening 
protein libraries for optimized proteins with desirable biological functions, such as antibodies with high binding affinity and low 
immunogenicity in humans. In one embodiment, a method is provided for constructing a 
library of 
antibody sequences based on a three dimensional structure of a lead 
antibody. The method comprises: providing an 
amino acid sequence of the variable region of the 
heavy chain (VH) or light chain (VL) of a lead 
antibody, the lead antibody having a known three dimensional structure which is defined as a lead structural template; identifying the 
amino acid sequences in the CDRs of the lead antibody; selecting one of the CDRs in the VH or VL region of the lead antibody; providing an 
amino acid sequence that comprises at least 3 consecutive amino acid residues in the selected CDR, the selected amino acid sequence being a lead sequence; comparing the lead sequence profile with a plurality of tester 
protein sequences; selecting from the plurality of tester 
protein sequences at least two 
peptide segments that have at least 10% 
sequence identity with lead sequence, the selected 
peptide segments forming a hit 
library; determining if a member of the hit 
library is structurally compatible with the lead structural template using a scoring function; and selecting the members of the hit library that 
score equal to or better than or equal to the lead sequence. The selected members of the hit library can be expressed 
in vitro or 
in vivo to produce a library of 
recombinant antibodies that can be screened for novel or improved function(s) over the lead antibody.