Linear B-Cell Epitope Prediction for In Silico Vaccine Design: A Performance Review of Methods Available via Command-Line Interface.

Linear B-cell epitope prediction research has received a steadily growing interest ever since the first method was developed in 1981. B-cell epitope identification with the help of an accurate prediction method can lead to an overall faster and cheaper vaccine design process, a crucial necessity in the COVID-19 era. Consequently, several B-cell epitope prediction methods have been developed over the past few decades, but without significant success. In this study, we review the current performance and methodology of some of the most widely used linear B-cell epitope predictors which are available via a command-line interface, namely, BcePred, BepiPred, ABCpred, COBEpro, SVMTriP, LBtope, and LBEEP. Additionally, we attempted to remedy performance issues of the individual methods by developing a consensus classifier, which combines the separate predictions of these methods into a single output, accelerating the epitope-based vaccine design. While the method comparison was performed with some necessary caveats and individual methods might perform much better for specialized datasets, we hope that this update in performance can aid researchers towards the choice of a predictor, for the development of biomedical applications such as designed vaccines, diagnostic kits, immunotherapeutics, immunodiagnostic tests, antibody production, and disease diagnosis and therapy.

Hydrogen bonds in protein-DNA complexes: where geometry meets plasticity.

Recognition of a DNA sequence by a protein is achieved by interface-coupled chemical and shape complementation. This complementation between the two molecules is clearly directional and is determined by the specific chemical contacts including mainly hydrogen bonds. Directionality is an instrumental property of hydrogen bonding as it influences molecular conformations, which also affects DNA-protein recognition. The prominent elements in the recognition of a particular DNA sequence by a protein are the hydrogen-bond donors and acceptors of the base pairs into the grooves of the DNA that must interact with complementary moieties of the protein partner. Protein side chains make most of the crucial contacts through bidentate and complex hydrogen-bonding interactions with DNA base edges hence conferring remarkable specificity.