TABLE 3.

List of important in silico peptide modeling servers.

Type	Brief description	URL	References
Hmmstr/Rosetta	The HMMSTR/Rosetta Server predicts the structure of proteins from the sequence: secondary, local, supersecondary, and tertiary	http://www.bioinfo.rpi.edu/~bystrc/hmmstr/about.html	Bystroff et al., 2000; Bystroff and Shao, 2002
Protinfo	Protinfo PPC is a web server that predicts atomic level structures of interacting proteins from their amino-acid sequences	http://protinfo.compbio.washington.edu/ppc/	Hung et al., 2005; Kittichotirat et al., 2009
Pepstr	This server predicts the tertiary structure of short peptides with sequence length varying between 7 to 25 residues	http://www.imtech.res.in/raghava/pepstr/	Kaur et al., 2007
FlexPepDock	The Rosetta FlexPepDock protocol for high-resolution docking of flexible peptides which mainly consists of two alternating modules that optimize the peptide backbone and rigid body orientation, respectively, using the Monte-Carlo with Minimization approach.	http://flexpepdock.furmanlab.cs.huji.ac.il/	Raveh et al., 2010
PepLook	Peplook server, an efficient tool to predict peptide conformation	https://orbi.uliege.be/handle/2268/135016	Beaufays et al., 2012
PepSite	This server is a tool for accurate prediction of peptide binding sites on protein surfaces	http://pepsite2.russelllab.org	Trabuco et al., 2012
Pep-Fold	PEP-FOLD is a de novo approach aimed at predicting peptide structures from amino acid sequences. This method, based on structural alphabet letters	https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD/	Maupetit et al., 2009; Thevenet et al., 2012
Pep-Fold3	PEP-FOLD3 latest evolution comes with a new 3D generation engine, based on a new Hidden Markov Model sub-optimal conformation sampling approach, faster by one order of magnitude than the previous greedy strategy, while not affecting performance	https://bioserv.rpbs.univ-paris-diderot.fr/services/PEP-FOLD3/	Lamiable et al., 2016