Computational Prediction of the Comprehensive SARS-CoV-2 vs. Human Interactome to Guide the Design of Therapeutics

Kevin Dick; Kyle K Biggar; James R Green

The SPRINT predictor is conceptually similar to PIPE; SPRINT aggregates evidence from previously known PPI interactions, depending on window similarity with the query protein pair, to inform its prediction scores [7] . SPRINT leverages a spaced seed approach for determining protein window sequence similarity, where each position in the two windows must either be identical, or do not matter, as defined by the match/don't_care bits of the spaced seeds. Furthermore, protein sequences are encoded using five bits per amino, enabling the use of highly efficient (SIMD) bitwise operations to rapidly compute protein window similarities and, thereby, score predictions [7] . Unfortunately, the present version of the SPRINT algorithm is not designed to explicitly handle inter-and cross-species prediction, nor to predict the specific subsequence site of interaction between a given pair of proteins. Nonetheless, it is among the only PPI predictors capable of predicting comprehensive interactomes in a timely manner and was demonstrated to outperform other PPI predictors, including the PIPE2 algorithm [7] .