Modelling TLR inhibition and promotion

Current work in the Lab aims to determine why some 3-mer sequences inhibit TLR7 while others do not. To achieve this, (PhD Student) has been running molecular dynamics simulations (MD) of TLR7 complexed with R848 (site 1) and all possible 3-mer RNA sequences with both natural and 2'Omethyl phosphothioate backbones (site 2). He is looking for a structural signal as to whether a given 3-mer sequence inhibits or not as finding this would provide an understanding of the molecular mechanism by which the novel RNAs modulate TLR7 and allow for in-silico screening of additional RNA sequences and chemistries.