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Metzler WJ, Valentine K, Roebber M, Friedrichs MS, Marsh DG, Mueller L, Determination of the three-dimensional solution structure of ragweed allergen Amb t V by nuclear magnetic resonance spectroscopy. Biochemistry. 1992 Jun 9;31(22):5117-27.
Where: AlnS= Alignment start position, AlnE= Alignment end position, EnvS= Envelope start position, EnvE= Envelope end position.
Predicted B-Cell epitope using BCEP method for Amb t 5
Probe radius : 1.400
POLAR area/energy = 2293.65
APOLAR area/energy = 4923.89
Total area/energy = 7217.53
Number of surface atoms = 419
Number of buried atoms = 137
Residues Predicted with high probability (in top five patches) are: 53,56,57,58,54,55,36,37,38,39,50,62,65,69,1,40 , and medium probability (next top five patches) are : 40,42,43,48,49,63,64,67,31,32,33,34,35,66,70,71 . Predicted residues are shown in red and green color stick representation.
Original PDB file with surface residue
only. All amino acid residue are replaced by their CB atom, in case of GLY CA atom is used. Solvent accessible surface area of each residue is stored in last
column of the PDB file.
Patch drawn around the residues by patch analysis are stored in this file
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area), Col 4: Sum(Psur*Area), Col 5: Total Residue, Col 6: Interface score, Col 7: Surface Score, Col 8: Max Interface Score, Col 9: Minimum Interface Score
Residues predicted by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Res Number Col 4: Neigbouring Res Name,
Col 5: Sum(Pint*Area). Col 6: Sum(PSur*Area), Col 7: Sum(Area), Col 8: Similar no of residue in patch (e.g CYS, CYS = 2)
All residues scored by patch analysis are stored in this file.
How to read: Col 1: Patch No. Col 2: Center Res Name. Col 3: Sum(Pint*Area)/sum(Area), Col 4: Sum(Psur*Area)/sum(Area), Col 5: Total Residue
[For BCEP predicted results, please cite our websites http://fermi.utmb.edu/ http://curie.utmb.edu/ for your future publications (Negi et al., Bioinformatics, 23, 3397-3399, 2007 , Negi et al., J. Mol. Model., 13, 1157-1167, 2007; Negi et al., J. Mol. Model., 12, 921-929, 2006)]
List of B-cell epitopes predicted by BepiPred method using a window size of 9 amino acids Peptides predicted from BepiPred method can be used to search related peptides in SDAP using PD search and Cross-React method. Please note: BepiPred Epitopes are predicted using BepiPred webserver implemented in IEDB Analysis Resource at http://tools.iedb.org/main/bcell/
Cleck here for epitopes predicted by BepiPred method Amb t 5 - Epitope Information from published data