Spatial and Sequential Topological Analysis of Molecular Dynamics Simulations of IgG1 Fc Domains

Monoclonal antibodies are utilized in a wide range of biomedical applications. The NIST monoclonal antibody is a resource for developing analysis methods for monoclonal antibody based biopharmaceutical platforms. Techniques from topological data analysis quantify structural features such as loops and tunnels which are not easily measured by classical data analysis methods. In this paper, we introduce the Gaussian CROCKER column differences (GCCD) matrix, which augments standard topological data analysis summaries with biological sequence information. We use GCCD matrices to successfully differentiate between glycosylated and aglycosylated conformations from molecular dynamics simulations of the NIST monoclonal antibody Fc domain. We are optimistic that other researchers will be able to utilize GCCD matrices to quantify multiscale spatial and sequential features.