Force field comparison through computational analysis of capsular polysaccharides of Streptococcus pneumoniae serotypes 19A and F

Abstract

Modern Molecular Dynamics force fields, such as the CHARMM36 and GLYCAM06carbohydrate force fields, are parametrised to reproduce behaviours for specific molecules under specific conditions in order to be able to predict the behaviour of similar molecular systems, where there is often no experimental data. Coupled with the sheer number available, this makes choosing the appropriate force field a formidable task. For this reason it is important that modern force fields be regularly compared. Streptococcus pneumoniae is a cause of invasive pneumococcal disease (IPD) such as pneumonia and meningitis in children under five. While there are over 90 pneumococcal serotypes only a handful of these are responsible for disease. Immunisation with the conjugate vaccine PCV7, has markedly decreased invasive pneumoccocal disease. Following PCV7 immunisation, incidences of non-vaccine serotypes, especially serotype19A, have increased.