title: Computational Tools for Aiding Rational Antibody Design.
abstract: Antibodies are a group of proteins responsible for mediating immune reactions in vertebrates. They are able to bind a variety of structural motifs on noxious molecules tagging them for elimination from the organism. As a result of their versatile binding properties, antibodies are currently one of the most important classes of biopharmaceuticals. In this chapter, we discuss how knowledge-based computational methods can aid experimentalists in the development of potent antibodies. When using common experimental methods for antibody development, we often know the sequence of an antibody that binds to our molecule, antigen, of interest. We may also have a structure or model of the antigen. In these cases, computational methods can help by both modeling the antibody and identifying the antibody-antigen contact residues. This information can then play a key role in the rational design of more potent antibodies.
authors.affiliation: Department of Statistics, University of Oxford, Oxford, UK.
authors.forename: Konrad
authors.initials: K
authors.lastname: Krawczyk
authors.affiliation: Department of Statistics, University of Oxford, Oxford, UK.
authors.forename: James
authors.initials: J
authors.lastname: Dunbar
authors.affiliation: Department of Statistics, University of Oxford, Oxford, UK. deane@stats.ox.ac.uk.
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000906:Antibodies / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D000941:Antigens / Q000737:chemistry / Q000276:immunology; D001665:Binding Sites; D022801:Complementarity Determining Regions / Q000737:chemistry / Q000276:immunology; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D000939:Epitopes / Q000737:chemistry / Q000276:immunology; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000235:genetics / Q000276:immunology; D007147:Immunoglobulin Light Chains / Q000235:genetics / Q000276:immunology; D051379:Mice; D008958:Models, Molecular; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011487:Protein Conformation; D015202:Protein Engineering / Q000379:methods*; D012984:Software; D013329:Structure-Activity Relationship; D064878:Web Browser
chemical_list: D000906:Antibodies; D000941:Antigens; D022801:Complementarity Determining Regions; D000939:Epitopes; D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains
keywords: Antibodies; Antibody VH–VL orientation; Antibody modeling; Antibody–antigen interactions; CDR loop modeling; Rational antibody design