Supplementary Figure 12: Total computation time for MaSIF-search and MaSIF-site for proteins of various sizes.
From: Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning
Proteins chains, of sizes: 50, 75, 100, 125, 200, 300, 500, were selected from the PDB. Each chain was run through both the MaSIF-site and MaSIF-search protocols, entailing: downloading the PDB, computing surfaces, input features, and coordinates, decomposing into patches, and computing MaSIF-site predictions and MaSIF-search descriptors. The y-axis shows the CPU user + System time + GPU time in minutes. GPU time consists of the time where the data is processed by the neural network, and was measured in real clock time (i.e. not GPU processor time). The total GPU time is low compared to the overall time, from 4 seconds for a 50-residue protein, to 12 seconds for a 500-residue protein. The line represents the regression fit to the n=7 data points and the shaded area represents the 95% confidence interval.
