Modeling of PH Domains and Phosphoinositides Interactions and Beyond

Pleckstrin homology (PH) domains form a large family of protein modules within membrane-targeting domains. PH domains can function as lipid-binding modules, and in particular bind with different specificities and affinities to phosphoinositides (PIs). Understanding the association of PH domains to PIs is critical for many aspects of cellular biology. Bioinformatics and computational modeling approaches have become standard tools to study the structure and dynamics of PH domains and PIs. In this review, recent advances in the binding specificity of PH domains and their interactions with PIs, using bioinformatics tools for the prediction of PIs binding sites, performing molecular dynamics simulations to study PH domains-PIs interactions, as well as the computational inhibitor design for PH domains guided signaling pathways have been discussed.