pyPept: a python library to generate atomistic 2D and 3D representations of peptides

Table 1 Examples of peptides using the three input formats BILN [14], HELM [13], and FASTA

BILN	HELM	FASTA
P-E-P-T-I-D-E	PEPTIDE1{P.E.P.T.I.D.E}$$$$V2.0	PEPTIDE
ac-D-T-H-F-E-I-A-am	PEPTIDE1{[ac].D.T.H.F.E.I.A.[am]}$$$$V2.0	None
C(1,3)-A-A-A-C(1,3)	PEPTIDE1{C.A.A.A.C} $PEPTIDE1,PEPTIDE1,1:R3-5:R3$$$V2.0	CAAAC
C(1,1)-A-A-A-C(1,2)	PEPTIDE1{C.A.A.A.C} $PEPTIDE1,PEPTIDE1,1:R1-5:R2$$$V2.0	CAAAC
A-G-Q-A-A-K(1,3)-E-F-I-A-A.G-L-E-E(1,3)	PEPTIDE1{A.G.Q.A.A.K.E.F.I.A.A}\| PEPTIDE2{G.L.E.E} $PEPTIDE1,PEPTIDE2,6:R3-4:R3$$$V2.0	None
N-Iva-F-D-I-meT-N-A-L-W-Y-Aib-K	PEPTIDE1{N.[Iva].F.D.I.[meT].N.A.L.W.Y.[Aib].K} $$$$V2.0	None

BILN’s support for specification of R-groups in bond formation means that linkage types can be easily specified. The BILN notation uses the monomer format m(n,i) to indicate that monomer m is a part of the cycle or branch assigned ID number n and connects via R-group i to a paired monomer p(n,j). i and j can be any R-groups involved in single bond linkage formation. Thus, the cyclization by cysteine linkage [C(1,3)] is by disulfide bond in the third example but by peptide bond [C(1,1), C(1,2)] in the fourth example

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