Constraint Network Analysis

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PDB ID
 		 OR    *
Analysis type: Single network - Single Structure
(Thermal unfolding simulation on a single network created from a single input structure)

Ensemble of networks - Ensemble of structures
(Thermal unfolding simulation on an ensemble of networks created from an ensemble of input structures)

Ensemble of networks - Single Structure
(Thermal unfolding simulation on an ensemble of networks created from a single input structure)
No. of network topologies
Simulation parameters: # of hydrophobic tethers remains constant during simulation (recommended)
# of hydrophobic tethers increases with increasing temperature
Hydrophobic method
Hydrophobic cutoff:

Constant value

Initial value

  

  

  Terminal value

E-cutoff for H-bonds:

Initial value

Stepsize

  

  Terminal value

Output settings:

Write stability map

  
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(Sample run for PDB ID 1NPC)
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 © CPC lab, 2012










*PLEASE NOTE:

Rules for uploaded file(s):

- Single structures must be in file format *.pdb.

- An ensemble of structures must be either a compressed multiple model PDB file (MODEL...ENDMDL) in format *.pdb.gz, or a compressed arbitrary-named folder (in format *.tgz or *.tar.gz or *.zip) including single PDB files.

- A compressed file of an ensemble must not be larger than 80 megabytes.

- Alternative sidechain conformations are not allowed.

- Missing side chains are not allowed.

- Hydrogens must have been added by the user.

Rules for PDB ID as input:

- No preparation needed.

- Incomplete residues will be fixed.

- Waters and ligands will be removed. To consider waters and ligands, please upload a file.

- Hydrogens will be added.

A single PDB file must not be larger than 15000 heavy atoms.

If the input structure contains an NMR ensemble, the first model will be used for CNA analysis.

Only protein atoms are allowed in the PDB file.

You do not need to provide an email adress, a link to the results will be returned. If you provide an email address, results will also be sent to this address. Please make sure that the email address is correct. Your e-mail will not be shared with any third parties. Input files, results, and e-mails will be stored up to 7 days after which they are permanently deleted. After this point, if you need support you will have to re-submit your calculations.


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Version 1.0