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PepCrawler is a fast RRT-based algorithm for high-resolution refinement and binding-affinity estimation of peptide inhibitors.

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Overview

PepCrawler is peptide docking algorithm used for:
    (i) Deriving a low energy binding-peptide from one of the proteins in a given protein-protein complex.
    (ii) Refinement of protein-peptide docking solution, relating to the peptide flexibility, using an RRT-Based method.
    (iii) Estimate binding affinity of a binding-peptide by scoring its energy plot funnel.
The algorithm requires as input a 3D complex structure (protein-protein OR protein-peptide) given as a pdb file

Input Fields

  • Input file content:
    Protein-protein complex OR protein-peptide complex.
    If the complex is protein-protein, PepCrawler will derive a suitable peptide from the ligand chain, and will use this peptide for calculations.

  • Complex PDB file:
    A file containing the complex in .pdb format.
    The file should contain a single pdb model of the complex. The algorithm adds hydrogen atoms to the complex so there is no need to add them manualy.

  • Receptor chain(s):
    One chain or more of the receptor protein.
    One letter for each chain.

  • Ligand chain:
    The chain of the ligand (peptide or protein).
    A single letter chain.

  • Energy parameters:
    Use enzyme-inhibitor (EI) for EI complexes. Use default for the rest.
    Make sure that the given ligand is indeed the inhibitor.

  • RRT run type:
    How wide is the RRT exploration.
    Use "full" for large exploration area (slower) or "restricted" for a small exploration area (faster).

  • Email address:
    PepCrawler results will be sent to you via Email. Please verify that you type in the correct email address.


    Output

    Once PepCrawler is done, an email will be sent to you containing a .zip file with all the result files.


    Run time

    PepCrawler run time depends on two main factors - peptide size and server workload.
    A single run should take not more than 40 minutes.