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# Table 1 PEPOP 2.0 methods and their main characteristics

From: PEPOP 2.0: new approaches to mimic non-continuous epitopes

Category | Sub category | Name | Full name | Composing elements | Characteristic | Epitope type mimetic |
---|---|---|---|---|---|---|

Sequential | FPS | Flanking Protein Sequence | protein sequence | Extension of a segment with the protein sequence | continuous | |

Nearest Neigbors | Prime methods | NN | Nearest Neighbors | segments in the natural orientation | Sequentially concatenation of NN segments | discontinuous |

uNN | upset NN | segments in the natural or reverse orientation | Sequentially concatenation of NN segments | |||

FNN | Flanking NN | segments in the natural orientation | Concatenation in turn C- and N-terminally of NN segments | |||

ONN | Optimized NN | segments in the natural orientation | Shortest path between the segments of NN method | |||

OFN | Optimized Flanking NN | segments in the natural orientation | Shortest path between the segments of FNN peptides | |||

OPP | Optimized Patched segments Path | segments in the natural orientation | Shortest path between the segments in a 10 Å-radius patch | |||

Prime methods with ALA linker | NNala | NN with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of NN method | ||

uNNala | upset NN with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of uNN method | |||

ONNala | Optimized NN with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of ONN method | |||

FNala | Flanking NN with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of FNN method | |||

OFNala | Optimized Flanking NN with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of OFN method | |||

OPPala | Optimized Patched segments path with ALA linker | segments in the natural orientation | ALA linkers inserted between segments of OPP method | |||

Prime methods with structural-based linker | NNsa | NN with SA linker | segments in the natural orientation | Linkers computed from SA inserted between segments of NN method | ||

ONNsa | Optimized NN with SA linker | segments in the natural orientation | Linkers computed from SA inserted between segments of ONN method | |||

FNsa | Flanking NN with SA linker | segments in the natural orientation | Linkers computed from SA inserted between segments of FNN method | |||

OFNsa | Optimized Flanking NN with SA linker | segments in the natural orientation | Linkers computed from SA inserted between segments of OFN method | |||

OPPsa | Optimized Patched segments Path with SA linker | segments in the natural orientation | Linkers computed from SA inserted between segments of OPP method | |||

Prime methods with superposed structural-based linker | NNsas | NN with SAS linker | segments in the natural orientation | Linkers computed from SAS inserted between segments of NN method | ||

ONNsas | Optimized NN with SAS linker | segments in the natural orientation | Linkers computed from SAS inserted between segments of ONN method | |||

FNsas | Flanking NN with SAS linker | segments in the natural orientation | Linkers computed from SAS inserted between segments of FNN method | |||

OFNsas | Optimized Flanking NN with SAS linker | segments in the natural orientation | Linkers computed from SAS inserted between segments of OFN method | |||

OPPsas | Optimized Patched segments path with SAS linker | segments in the natural orientation | Linkers computed from SAS inserted between segments of OPP method | |||

Graph Theory | SHP methods | SHPnat | SHP natural | segments in the natural orientation | Shortest path between segments using Dijkstra’s algorithm | |

SHPrev | SHP reverse | segments in the natural or reverse orientation | Shortest path between segments using Dijkstra’s algorithm | |||

SHPaa | SHP amino acids | amino acids | Shortest path between segments using Dijkstra’s algorithm | |||

TSP methods | TSPnat1 | TSP natural 1 | segments in the natural orientation | Shortest path between segments using Dantzig & Fulkerson’s algorithm and most favorable interacting parameters | ||

TSPnat2 | TSP natural 2 | segments in the natural orientation | Shortest path between segments using Dantzig & Fulkerson’s algorithm | |||

TSPnat3 | TSP natural 3 | segments in the natural orientation | Shortest path using Dantzig & Fulkerson’s algorithm according to the number of segments | |||

TSPnat4 | TSP natural 4 | segments in the natural orientation | Shortest path using Dantzig & Fulkerson’s algorithm including the 2 closest segments | |||

TSPrev1 | TSP reverse 1 | segments in the natural or reverse orientation | Shortest path using Dantzig & Fulkerson’s algorithm and most favorable interacting parameters | |||

TSPrev2 | TSP reverse 2 | segments in the natural or reverse orientation | Shortest path using Dantzig & Fulkerson’s algorithm | |||

TSPrev3 | TSP reverse 3 | segments in the natural or reverse orientation | Shortest path using Dantzig & Fulkerson’s algorithm according to the number of segments | |||

TSPrev4 | TSP reverse 4 | segments in the natural or reverse orientation | Shortest path using Dantzig & Fulkerson’s algorithm including the 2 closest segments | |||

TSPaa | TSP amino acids | amino acids | Shortest path using Dantzig & Fulkerson’s algorithm |