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Required input
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PATH-ENM server uses a newly developed mixed elastic network model (MENM) to generate transition paths between two given macromolecular structures (for details of the method see here or reference). The basic idea is to combine two ENM potentials (built from the two given structures) into a smoothly interpolated "mixed" potential, which has two minima (corresponding to the two given structures) and one saddle point (corresponding to the transition state). Then a minimal energy path is generated to connect the two end-state structures via the saddle point.
To run PATH-ENM, you are required to upload two PDB files for the two end-state 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.
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Upload the first PDB file (example)
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or paste the PDB file into the field below
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Upload the second PDB file (example)
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or paste the PDB file into the field below
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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
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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.
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Parameters setting
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The first parameter (number of residues per ENM node) sets the coarse-graining level of the ENM representation. Due to memory limitation, PATH-ENM will not run for an ENM with > 2000 nodes. If your protein has < 2000 amino acid residues, either option (1 or 2) is fine; If your protein has 2000 ~ 4000 amino acid residues, you should select 2; If your protein has > 4000 amino acid residues, contact us for help.
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.
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| coarse-graining level (number of residues per ENM node) |
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| distance cutoff for elastic interaction between CA atoms |
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