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Submit a job to iENM!

Required input

iENM server uses interpolated elastic network model (iENM) to generate a transition path between two given macromolecular structures (for details, see reference). To run iENM, you are required to upload two PDB files for the beginning and end structures. For a database of PDB structures, visit Protein Data Bank.

You can find an example here.

Note that only records starting with the keyword "ATOM" will be considered: only CA atoms of amino acids and P atoms of DNA/RNA nucleotides are read; everything else including water molecules (HOH, H2O, TIP3 and WAT) will be ignored. Your PDB files must be smaller than 2 MB, or else they will not be uploaded correctly!

Upload the first PDB file (example)
or paste the PDB file into the field below

Upload the second PDB file (example)
or paste the PDB file into the field below

Please enter a title for your job (it must be 4 alphanumeric characters). It will be used in the names of the output files.
job title

If you wish to be notified by email once your job is finished, please enter your e-mail address below (it will also allow us to send you diagnostic information in case your job fails). Othewise you will be given a URL to your job outputs upon submission of your job, which you can check back later. Your e-mail address will be used only for the above purpose and then it will be discarded unless you choose to receive updates about this server.


Click here if you wish to receive future updates about the AD-ENM server.

Parameters setting

The following parameter sets the cutoff distance for connecting two neighboring CA atoms by a spring. The cutoff distance for two neighboring P atoms is fixed to be 20 Angstrom, while for neighboring P and CA atoms it is set to be the average of the previous two values.

distance cutoff for elastic interaction between CA atoms

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