Complementarity determining regions loops

Two chains come together to form the binding surface of an antibody. Three loops from each domain, the complementarity-determining regions, form an essentially continuous surface that can vary tremendously in shape, charge, and other characteristics to allow particular antibodies to bind to molecules ranging from small molecules to... 

Abbreviations used in table MC - Monte Carlo aa - amino acid vdW - van der Waals potential Ig - immunoglobulin or antibody CDR - complementarity-determining regions in antibodies RMS -root-mean-square deviation r-dependent dielectric - distance-dependent dielectric constant e - dielectric constant MD - molecular dynamics simulation self-loops - prediction of loops performed by removing loops from template structure and predicting their conformation with template sequence bbdep - backbone-dependent rotamer library SCMF - self-consistent mean field PDB - Protein Data Bank Jones-Thirup distances - interatomic distances of 3 Ca atoms on either side of loop to be modeled. 

The next improvement was humanization - the grafting of the complementarity-determining regions (CDRs) of a mouse antibody onto a human framework [14]. For this purpose, a human framework is chosen from the database of human genes for Vh, another for Vl (k or X), and an ahgnment of the murine and human sequences is made. In addition to the CDRs themselves, differences in the framework must be taken into account (Fig. 2.2). For example, the so-caUed outer loop (some-... 

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