Computational Biophysics Section of the Laboratory of Computational Biology
National Heart, Lung, and Blood Institute
National Institutes of Health
Department of Health and Human Services
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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.
E-mail
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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Department of Health and Human Services
National Institutes of Health
National Heart, Lung, and Blood Institute
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