Statistical Analysis of Nanobody Sequences and Structures with Molecular Dynamics Simulation of Nanobody VHH

Abstract

Nanobodies, also known as single-domain antibodies, are an area of study due to their unique structure and small size. These antibodies, derived from camelids, consist only of heavy-chain domains, making them an excellent candidate for various therapeutic and diagnostic applications. This paper presents a statistical analysis of nanobody sequences and structures from existing databases and utilizes molecular dynamics (MD) simulation to model and assess the stability of a SARS-CoV-1 cross-reactive nanobody (6waq). By analyzing key metrics such as Root-Mean-Square Deviation (RMSD) and Root-Mean-Square Fluctuation (RMSF), this study provides insights into nanobody structural dynamics and potential optimizations for therapeutic use.