title: Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking.
abstract: Antibodies are a class of proteins indispensable for the vertebrate immune system. The general architecture of all antibodies is very similar, but they contain a hypervariable region which allows millions of antibody variants to exist, each of which can bind to different molecules. This binding malleability means that antibodies are an increasingly important category of biopharmaceuticals and biomarkers. We present Antibody i-Patch, a method that annotates the most likely antibody residues to be in contact with the antigen. We show that our predictions correlate with energetic importance and thus we argue that they may be useful in guiding mutations in the artificial affinity maturation process. Using our predictions as constraints for a rigid-body docking algorithm, we are able to obtain high-quality results in minutes. Our annotation method and re-scoring system for docking achieve their predictive power by using antibody-specific statistics. Antibody i-Patch is available from http://www.stats.ox.ac.uk/research/proteins/resources.
authors.affiliation: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK.
authors.forename: Konrad
authors.initials: K
authors.lastname: Krawczyk
authors.forename: Terry
authors.initials: T
authors.lastname: Baker
authors.forename: Jiye
authors.initials: J
authors.lastname: Shi
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Deane
mesh_terms: D000465:Algorithms; D000906:Antibodies / Q000737:chemistry* / Q000276:immunology*; D000941:Antigens / Q000276:immunology*; D001665:Binding Sites; D022801:Complementarity Determining Regions / Q000737:chemistry / Q000276:immunology; D019295:Computational Biology; D062105:Molecular Docking Simulation
chemical_list: D000906:Antibodies; D000941:Antigens; D022801:Complementarity Determining Regions
keywords: CDR; antibody; docking