title: MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.
abstract: BACKGROUND
  The de novo design of a novel protein with a particular function remains a formidable challenge with only isolated and hard-to-repeat successes to date. Due to their many structurally conserved features, antibodies are a family of proteins amenable to predictable rational design. Design algorithms must consider the structural diversity of possible naturally occurring antibodies. The human immune system samples this design space (2 1012) by randomly combining variable, diversity, and joining genes in a process known as V-(D)-J recombination.
  
  
  METHODS
  By analyzing structural features found in affinity matured antibodies, a database of Modular Antibody Parts (MAPs) analogous to the variable, diversity, and joining genes has been constructed for the prediction of antibody tertiary structures. The database contains 929 parts constructed from an analysis of 1168 human, humanized, chimeric, and mouse antibody structures and encompasses all currently observed structural diversity of antibodies.
  
  
  CONCLUSIONS
  The generation of 260 antibody structures shows that the MAPs database can be used to reliably predict antibody tertiary structures with an average all-atom RMSD of 1.9 Å. Using the broadly neutralizing anti-influenza antibody CH65 and anti-HIV antibody 4E10 as examples, promising starting antibodies for affinity maturation are identified and amino acid changes are traced as antibody affinity maturation occurs.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Pantazes
authors.forename: Costas D
authors.initials: CD
authors.lastname: Maranas
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D057134:Antibodies, Neutralizing / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D000914:Antibodies, Viral / Q000737:chemistry* / Q000235:genetics / Q000276:immunology*; D000915:Antibody Affinity; D030562:Databases, Protein; D015483:HIV Antibodies / Q000737:chemistry / Q000235:genetics / Q000276:immunology; D006801:Humans; D051379:Mice; D008958:Models, Molecular; D009975:Orthomyxoviridae / Q000276:immunology*; D015202:Protein Engineering; D017434:Protein Structure, Tertiary
chemical_list: D057134:Antibodies, Neutralizing; D000914:Antibodies, Viral; D015483:HIV Antibodies