Supplementary material for Discotope-2.0:

Description of the evaluation data set (excel file).

all.how (ALL entries merged) in HOW format.

An example of the HOW format is shown below

   151 1AFV.A
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEW
DRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSIL
.......................................................................H.LLHLLH.
LLL.L..............LLL.................................................

The first line contains the length of the antigen sequence and the PDB identifier (PDBID.CHAINID). The next lines give the amino acid sequence, and the last lines the epitope annotation. Dots in the annotation lines denote non-epitope residues and letters denote epitope residues. The letters refer to the chain id of the contacting heavy or light chain, respectively.

Individual entries in HOW format:

1YNT.F.how
2NYY.A.how
2NZ9.A.how
3I50.E.how
1Z3G.A.how
3RHW.D,E,A,B,C.how
3RI5.C,D,E,A,B.how
3RIA.B,E,A,C,D.how
3RIF.B,C,E,A,D.how
1AFV.A.how
3MJ9.A.how
1BGX.T.how
2R56.A,B.how
3BSZ.E,F.how
2I9L.I.how
1RVF.1,2,3.how
3G04.C.how
3KJ4.A.how
3O0R.B,C.how
2Q8A.A.how
2Q8B.A.how
3GI8.C.how
3GI9.C.how
3NCY.C,D.how
2DD8.S.how
2GHW.A.how
3BGF.S.how
2XQY.A.how
2NR6.A.how
3LIZ.A.how
2ZJS.Y.how
2UZI.R.how
2VH5.R.how
2XTJ.A.how
3H42.B,A.how
3R1G.B.how
2ZCH.P.how
2ZCK.P.how
2ZCL.P.how
3BN9.B.how
3GRW.A.how
3L95.Y.how
3MXW.A.how
2R4R.A.how
2R4S.A.how
3KJ6.A.how
2OZ4.A.how
2FD6.U.how
3G6J.B,A.how
3FMG.A,B,C.how
3PGF.A.how
2J88.A.how

References

Reliable B cell epitope predictions: Impacts of method development and improved benchmarking. Submitted for publication
Jens Vindahl Kringelum, Claus Lundegaard, Ole Lund, and Morten Nielsen