Table 3.

Computational-based approaches for studying PLI

	Large-scale analysis	Molecular mechanism
Data required	High-throughput PLI screening (protein or lipid microarrays).	Structural and kinetic details of PLI (NMR, FRET, etc.).
Objective	Systematic catalog and analysis of PLIs in an organism/phenotype.	Prediction of PLI, PLI-interface, and dynamics. Exploring the molecular mechanism of PLI.
Techniques	Sequence comparison; statistical analysis; network analysis/ inference [64].	Machine learning (classification) [93–95].	Molecular dynamic simulation [96–102].
Usage	Estimation of the accuracy, sensitivity, and bias of high-throughput screening; inference of PLI function [64].	Prediction of binding interface/motif based on sequence [94,95]	Study the structural basis of PLI [102]; explore functional specificity of PLI [100].
Future perspective	Incorporation of PPI and PDI to achieve comprehensive understanding of the functional mechanisms of PLIs.	Multi-scale approaches that model and combine different levels of molecular information to achieve better understanding of the molecular mechanisms of PLI.