On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations.

ABSTRACT: The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relie

SUBMITTER: Conti S 

PROVIDER: S-EPMC9397028 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature