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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
  1. ALA alanine, NN nearest neighbor, SA structural alphabet, SAS superposed structural alphabet, SHP SHortest Path algorithm, TSP Traveling Salesman Problem algorithm