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 |
|---|---|---|---|---|---|---|
| Â | 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 |