Assessment of fully automated antibody homology modeling protocols in molecular operating environment.
The success of antibody-based drugs has led to an increased demand for predictive computational tools to assist antibody engineering efforts surrounding the six hypervariable loop regions making up the antigen binding site. Accurate computational modeling of isolated protein loop regions can be quite difficult; consequently, modeling an antigen binding site that includes six loops is particularly challenging. In this work, we present a method for automatic modeling of the FV region of an immunoglobulin based upon the use of a precompiled antibody x-ray structure database, which serves as a source of framework and hypervariable region structural templates that are grafted together. We applied this method (on common desktop hardware) to the Second Antibody Modeling Assessment (AMA-II) target structures as well as an experimental specialized CDR-H3 loop modeling method. The results of the computational structure predictions will be presented and discussed.
['Maier|Johannes K X|JK|', 'Labute|Paul|P|']
D000818:Animals D000906:Antibodies D022801:Complementarity Determining Regions D030562:Databases, Protein D006801:Humans D007135:Immunoglobulin Variable Region D008958:Models, Molecular D011487:Protein Conformation D012984:Software D040681:Structural Homology, Protein
homology modeling antibody engineering CDR-H3 loop modeling antibody structure comparative modeling loop enrichment loop refinement