Immunoglobulin (Ig) amino acid sequences are highly conserved and ofte
n have sequence homology ranging from 70 to 95%. Antigen binding fragm
ents (Fab), variable region fragments (Fv), and single chain Fv (scFv)
of more than 50 myeloma proteins and monoclonal antibodies (mAb) have
been crystallized and display a high degree of structural similarity.
Based on this observation, several homology modeling approaches have
been developed for the prediction of Fab and Fv structures prior to th
eir experimental determination. We have extracted features from existi
ng Ig sequences, 44 known Fab and Fv structures to create an automated
AntiBody structure GENeration (ABGEN) algorithm for obtaining structu
ral models of antibody fragments. ABGEN utilizes a homology based scaf
folding technique, and includes the use of invariant and strictly cons
erved residues, structural motifs of known Fab, canonical features of
hypervariable loops, torsional constraints for residue replacements an
d key inter-residue interactions. The validity of the ABGEN algorithm
has been tested using a five-fold cross validation with the existing F
ab structures. Molecular mechanics and dynamics methods have been impl
emented with ABGEN models to accurately predict two Fab structures of
anti-sweetener antibodies prior to crystallographic determinations.