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Required input
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The DC-ENM server builds a structural model for a protein at an unknown state by using:
1. the lowest normal modes that are solved from an elastic network model
(ENM) built from an initial-state structure;
2. a number of distance constraints (DC) for the unknown state (measured by NMR, FRET, etc).
For details of the method please see: Zheng, W. & Brooks, B.R. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophys. J. 90, 4327-36 (2006)
(pubmed).
You can find an example here.
To get started, please upload a PDB file for the initial-state structure.
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 and DC files must be smaller than 2 MB, or else they will not be uploaded correctly!
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Upload a PDB file
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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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Now please upload a data file containing the pairwise distance constraints for the end-state structure in the following format (one DC entry per line):
[chain_id 1][residue_number 1],[chain_id 2][residue_number 2],[target_distance],[weight]
Note:
chain_id 1(2): the chain id (given in column 22 of a PDB file) of the first(second) residue (use '_' if the chain id is NULL);
residue_number 1(2): the residue number (given in column 23-26 of a PDB file) of the first(second) residue;
target_distance: the target distance for the given DC pair;
weight: a value between 0 and 1 to weigh the DC in the fitting score function.
Example: To add a DC between the CA atoms of a pair of residues (100, 200) with target distance 10.0 and weight 1.0 (if chain id is NULL), enter the following line:
_100,_200,10.0,1.0
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Upload a DC data file
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or paste the DC data file into the field below
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Optional input
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You may want to upload a second PDB file for the end-state structure to compare it with the model built by DC-ENM:
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Upload a second PDB file
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or paste the PDB file into the field below
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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 webserver.
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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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 is the number of lowest normal modes to be used for fitting the given DCs.
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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| Number of modes used for fitting DC |
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| Distance cutoff for elastic interaction between CA atoms |
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