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Generate missing loops: alternative conformations

Generate missing loops in the input PDB file (of length less than 21) using E.W. Knapp's algorithm (PDF).

This implies a definitely idealized (but plausible) geometry of the peptide bond for the constructed loop.
The program will detect automatically the missing residues from the numbering and build them until the CB atom.

To assign the sequence of the missing loop(s), the program will rely on information in the PDB file (lines REMARK 265); if this information is missing, they will be assigned to ALA residue type.
After completion of this program, which only builds the mainchain atoms, you still need to run "Fix missing side-chains" to complete the coordinates of atoms beyond the CB atom.
If you would like something else, you have two options:
-change the amino acid type in the PDB file using the editor and submit the a job to "Fix missing side chains"
-prepare an alignment between the sequence of the old PDB file and the desired sequence and submit a job to "Decorate"

Your email adress: (Recommended, for notification)


Job title (Only alphanumerical characters)


PDB input file Ex: Example


Number of solutions (currently limited to 10)



Input data formats

  • The job title is just for your own identification, but note that it will show up in the public job queue (but your results will not be public).

  • The coordinate file should be in PDB format, with only a single structure (no multiple models). Atoms marked with alternate residue flags will be removed. Hetero-atoms (HETATM) will be copied to the output file.

  • Limitations At this stage the program only works with proteins with a single chain. Also, it cannot build N-termini or C-termini, as it needs two anchor points to build a loop. The maximum loop size that can be constructed is 21.





  Marc Delarue http://lorentz.dynstr.pasteur.fr
Page last modified 18:54 May 05, 2016.