ArticleBMC bioinformatics2013
MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A universal in silico V(D)J recombination strategy for developing humanized monoclonal antibodies.Journal of nanobiotechnology · 2022Article
- OptMAVEn-2.0: De novo Design of Variable Antibody Regions against Targeted Antigen Epitopes.Antibodies (Basel, Switzerland) · 2018Article
- RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.PLoS computational biology · 2018Article
- De novo design of antibody complementarity determining regions binding a FLAG tetra-peptide.Scientific reports · 2017Article
- Computational de novo design of antibodies binding to a peptide with high affinity.Biotechnology and bioengineering · 2017Article
- High-accuracy modeling of antibody structures by a search for minimum-energy recombination of backbone fragments.Proteins · 2017Article
- AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.Proteins · 2015Article
- Rigidity Emerges during Antibody Evolution in Three Distinct Antibody Systems: Evidence from QSFR Analysis of Fab Fragments.PLoS computational biology · 2015Article
- Mammalian cell culture process for monoclonal antibody production: nonlinear modelling and parameter estimation.BioMed research international · 2015Article
- Protein folding and de novo protein design for biotechnological applications.Trends in biotechnology · 2014Review
- OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.PloS one · 2014Article
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2 authors.
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Abstract
backgroundThe 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. DESCRIPTION: 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.
conclusionsThe 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.
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