Table 1. Existing peptide-protein complex modeling methods.

Method	Category	Availability	Requires binding site	Initial peptide conformation	Tested (max) amino acidsa
Hetenyi et al. [20]	Docking	No	No	TINKER [33]	4
Liu et al. [22]	Docking	No	Yes	Bound conformation	16
Rosetta FlexPepDock ab-initio [23, 24]	Docking	Yes	Yes	Predicted fragments	15 (30)
HADDOCK [25]	Docking	Yes	Yes	α-helix, extended, polyproline	15
pepATTRACT [26]	Docking	Yes	No	α-helix, extended, polyproline	15
CABS-DOCK [27]	Docking	Yes	No	Random	15 (30)
MdockPeP [21]	Docking	No	No	Sequence-based search	15
DynaDock [17]	MD	No	Yes	Bound conformation	16
Dagliyan et al. [18]	MD	No	No	Bound conformation	13
AnchorDock [19]	MD	No	No	Extended/MD	15

^a: Tested is the longest peptide in the published test set and max is the maximum length allowed by the web server.