Table S1 Adaption from former Pep-3D-Search. To improve the time efficiency of Pep-3D-Search, we made few adaptations from the former one. These includes a quicker approach in the generating a random background distribution for scoring the best aligned paths from graph search as well as the adjustment of the key parameters. As is shown in the Table S1 , the performance improved on 3IU3_I, 1D4V_B in the adapted Pep-3D-Search on which the former Pep-3D-Search failed to predict any epitopic amino acids. On average, the new Pep-3D-Search has similar sensitivity and specificity, but higher precision. (DOC)  Autophagy: More Than a Nonselective Pathway Autophagy is a catabolic pathway conserved among eukaryotes that allows cells to rapidly eliminate large unwanted structures such as aberrant protein aggregates, superfluous or damaged organelles, and invading pathogens. The hallmark of this transport pathway is the sequestration of the cargoes that have to be degraded in the lysosomes by double-membrane vesicles called autophagosomes. The key actors mediating the biogenesis of these carriers are the autophagy-related genes (ATGs). For a long time, it was assumed that autophagy is a bulk process. Recent studies, however, have highlighted the capacity of this pathway to exclusively eliminate specific structures and thus better fulfil the catabolic necessities of the cell. We are just starting to unveil the regulation and mechanism of these selective types of autophagy, but what it is already clearly emerging is that structures targeted to destruction are accurately enwrapped by autophagosomes through the action of specific receptors and adaptors. In this paper, we will briefly discuss the impact that the selective types of autophagy have had on our understanding of autophagy. Three different pathways can deliver cytoplasmic components into the lumen of the lysosome for degradation. They are commonly referred to as autophagy (cell "self-eating") and include chaperone-mediated autophagy (CMA), microautophagy, and macroautophagy. CMA involves the direct translocation of specific proteins containing the KFERQ pentapeptide sequence across the lysosome membrane [1, 2] . Microautophagy, on the other hand, entails the invagination and pinching off of the lysosomal limiting membrane, which allows the sequestration and elimination of cytoplasmic components. The molecular mechanism underlying this pathway remains largely unknown. The only cellular function that so far has been indisputably assigned to microautophagy is the turnover of peroxisomes under specific conditions in fungi [3] . Recently, it has been reported the existence of a microautophagy-like process at the late endosomes, where proteins are selectively incorporated into the vesicles that bud inward at the limiting membrane of these organelles during the multivesicular bodies biogenesis [4] . In contrast to CMA and microautophagy, macroautophagy (hereafter referred to as autophagy) entails the formation of a new organelle, the autophagosome, which allows the delivery of a large number of different cargo molecules into the lysosome.