Method for GalaxyPepDock

GalaxyPepDock predicts 3D protein-peptide complex structures from input protein structure and peptide sequence by combining information on similar interactions found in the structure database and energy-based optimization.

You can download a standalone version at here.

Inputs for GalaxyPepDock

User Information

First, you have to enter the following information required for modeling.
  • Job name: Enter job name for your recognition.
  • E-mail address: GalaxyWEB server will send progress reports of your job.

Input Protein Structure and Peptide Sequence

You have to provide a protein structure in the PDB format and a peptide sequence in the FASTA format.

Outputs for GalaxyPepDock

User input

Predicted protein-peptide complex structures

(Template structures are shown in light colors)
The 10 best models can be downloaded or viewed in PV.

Additional information

Sequences & alignments: Protein alignment (result of structure alignment) and peptide alignment (result of sequence alignment with more weights on interacting residues in the template)
Protein structure similarity: Similarity of the input protein structure to the selected template structure
Interaction similarity score: Similarity of the amino acids of the target complex aligned to the contacting residues in the template structure to the template amino acids
Estimated accuracy: The estimated fraction of correctly predicted binding site residues.
The prediction accuracy is estimated from a linear model of the relationship between the fraction of correctly predicted binding site residues and the template-target similarity (measured by the protein TM-score and S_inter) obtained by a linear regression of the PeptiDB test set results.
Estimated accuracy = max[0, min(1, -0.35576 + 0.98280*TM-score + 0.00223*S_inter)]
If estimated accuracy is closed to zero, it is suggested to use other ab initio protein-peptide docking tools.
Predicted binding site residues in protein: The residues that have at least one heavy atom at a distance of less than 5 angstroms from any peptide heavy atoms in the generated model

References for GalaxyPepDock
  • H. Lee, L. Heo, M. S. Lee, and C. Seok, GalaxyPepDock: a protein-peptide docking tool based on interaction similarity, Nucleic Acids Res. 43 (W1), W431-W435 (2015). [LINK]