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Submit a job to AD-ENM!


Required input

AD-ENM server provides a spectrum of analyses for the dynamics of an elastic network model (ENM) built from a given macromolecular structure. Therefore, you must upload a PDB file (example) for that structure to start your run! For a database of PDB structures, visit Protein Data Bank.
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 a PDB file
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

Optional input

In the following cases you may want to upload a second PDB file: Please check one
Option 1: If a second macromolecular structure is known, the Elastic Network Model may be used to determine the contribution of each normal mode to the observed conformational changes. In this case the uploaded PDB file should contain the ATOM records for the second macromolecular structure (example).
Option 2: If a new conformation of a subset of residues (pocket residues) is known, and you want to study how the whole macromolecule changes its conformation in response to the pocket deformation toward the new conformation. In this case the uploaded PDB file should only contain the ATOM records for the CA/P atoms of the pocket residues (example).
Option 3: If you only know the identities of a subset of residues (so called pocket residues) but you don't know their new conformation, you can check this option. This analysis examines the mean square fluctuation (MSF) of the pocket residues, and it identifies those dynamically important residues whose perturbation may affect the pocket MSF significantly, and those relevant normal modes that contribute significantly to the pocket MSF. In this case you can just upload a PDB file containing the ATOM records for the CA/P atoms of the pocket residues with the (x,y,z) fields set to (9999.00, 9999.00, 9999.00) (example).

You can find an example here.

Upload a second PDB file
or paste the PDB file into the field below

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 webserver.

E-mail

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



Output specification

For output, there will be one PDB file per mode containing the structural model deformed in the direction of each normal mode. You may specify the number of lowest modes to output and their amplitude in displacement:
Number of lowest modes to output
Amplitude of displacement per mode
Number of frames to generate


Parameters setting

If you are new to ENM, you are advised to keep the default settings of the parameters below! Otherwise please follow the instructions below:

The first parameter adjusts the level of coarse-graining in the ENM you build. Basically, every two points within the given distance cutoff are merged into a big pseudo-atom. If the macromolecular system is not too large, you can set it to zero and no such merging happens; if the macromolecular system is really large, you may set it 4 or even larger to reduce the size of ENM and attain shorter CPU time. AD-ENM will not run if the ENM size is too large (over 3000 points).

The second 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 coarse-graining
Distance cutoff for elastic interaction between CA atoms




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