ModiBodies: A computational method for modifying nanobodies in nanobody-antigen complexes to improve binding affinity and specificity.

ABSTRACT: Nanobodies are special derivatives of antibodies, which consist of single domain fragments. They have become of considerable interest as next-generation biotechnological tools for antigen recognition. They can be easily engineered due to their high stability and compact size. Nanobodies have three complementarity-determining regions, CDRs, which are enlarged to provide a similar binding surface to that of human immunoglobulins. Here, we propose a benchmark testing algorithm that uses 3D structures of already existing protein-nanobody complexes as initial structures followed by successive mutations on the CDR domains. The aim is to find optimum binding amino acids for hypervariable residues of CDRs. We use molecular dynamics simulations to compare the binding energies of the resulting compl

SUBMITTER: Hacisuleyman A 

PROVIDER: S-EPMC7334311 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature