Links related to peptide tertiary structure prediction

1 PEPstrMOD Peptide tertiary structure prediction server with non-natural modifications.
2 PEPstr Peptide tertiary structure prediction server.
3 PEP-FOLD An updated de novo peptide structure prediction server.

Links related to resources for Molecular Dynamics Simulations

1 GROMACS GROMACS (GROningen MAchine for Chemical Simulations) is a molecular dynamics package primarily designed for simulations of proteins, lipids and nucleic acids.
2 AMBER Amber is a package of programs for molecular dynamics simulations of proteins and nucleic acids.
3 Forcefield_NCAA AMBER Forcefield Parameters for Non-canonical Amino Acids.
4 Forcefield_PTM AMBER Forcefield Parameters for Post-translational Modifications.
5 SwissSideChain A molecular and structural database of non-natural side chains.
6 Vienna-PTM web server A toolkit for MD simulations of protein post-translational modifications

Other links related to peptides

1 PEP-SiteFinder A service to identify candidate protein-peptide interaction sites.
2 PepBind A comprehensive database and computational tool for analysis of protein-peptide interactions.
3 PeptiSite A structural database of peptide binding sites.
4 DOMINO A database of domain peptide interactions.
5 SPdb Signal peptide database.
6 PCSS Server Peptide classification using sequence and structure
7 SignalP A webserver for discriminating signal peptides from transmembrane regions.
8 Rosetta FlexPepDock High resolution modeling of peptide-protein interactions.
9 PeptiMap Detection of peptide binding sites on protein surfaces.

Peptide based resources from our group

1 SATPdb A database of structurally annotated therapeutic peptides
2 AntiAngioPred A server for prediction of anti-angiogenic peptides
3 CancerPPD A database of anticancer peptides
4 AHTPDB A platform for analysis and presentation of antihypertensive peptides.
5 Hemolytik A database of experimentally determined hemolytic and non-hemolytic peptides.
6 ParaPep A database of anti-parasitic peptides.
7 CPPsite A curated database of cell penetrating peptides.
8 CellPPD In silico approaches for designing highly effective cell penetrating peptides.
9 TumorHoPe A database of tumor homing peptides.
10 TumorHPD Computational approaches for designing tumor homing peptides.
11 ToxinPred In silico approach for predicting toxicity of peptides and proteins.
If you are using PEPstrMOD, please cite the following articles:
i) Singh, S., Singh, H., Tuknait, A., Chaudhary, K., Singh, B., Kumaran, S. and Raghava, G.P.S. (2015) PEPstrMOD: structure prediction of peptides containing natural, non-natural and modified residues. Biology Direct 10:73.
ii) Kaur, H., Garg, A. and Raghava, G.P.S. (2007) PEPstr: A de novo method for tertiary structure prediction of small bioactive peptides. Protein Pept Lett. 14:626-30.
Click Here for PEPstrMOD Manual