Jernigan Laboratory
hdANM
Search Close Search
Toggle Menu

Online Server for hdANM model using PACKMAN

Information & Instructions

This webpage will provide an interface for hdANM online. Please refer to the following research article to know more about the parameters and citation:

Pranav M. Khade, Domenico Scaramozzino, Ambuj Kumar, Giuseppe Lacidogna, Alberto Carpinteri, Robert L. Jernigan, hdANM: a new comprehensive dynamics model for protein hinges, Biophysical Journal, 2021, https://doi.org/10.1016/j.bpj.2021.10.017

For more information on the PACKMAN visit https://github.com/Pranavkhade/PACKMAN

NOTE

  1. For hinge prediction on the input protein for the HNG file, use PACKMAN GUI or PACKMAN webserver. GUI provides the HNG file, but the webserver gives information that the user can make into the .hng file.
  2. Please fill out all the tabs (Input, Arguments, and Movie) to run the hdANM webserver.
If provided, the PBD with this ID will be downloaded and used as the input file.
This server allows C-alpha atoms only because of the computational constraints; however, the all-atom model can run using PACKMAN - hdANM API on the user's computer. Please refer to the following page. https://py-packman.readthedocs.io/en/latest/tutorials/hdANM.html#tutorials-hdanm
captcha
Enter the text from the image into the box.
Distance cutoff for the ANM.
Power of the distance in non-parametric ANM.
HNG

hdANM also requires the user to provide the .hng file containing the information about which parts of the protein are hinges and which parts are rigid domains. This information can be obtained from the PACKMAN’s hinge prediction algorithm. Please read the following for more details: https://packman.bb.iastate.edu/

You can either upload this as a file or enter the values manually below

Hinge Information file format (.hng) Example:

1exr.pdb_A	D1	1:70
1exr.pdb_A	H1	71:90
1exr.pdb_A	D2	91:150

The first column in the .hng file is Filename_ChainID, the second column is Domain/Hinge ID, and the third column is the residues in the particular domain/hinge.

The .hng file is tab-separated. (Tabs separate columns)

Filename_ChainID
Domain/Hinge ID
Residues
Filename_ChainID
Domain/Hinge ID
Residues
Filename_ChainID
Domain/Hinge ID
Residues
Filename_ChainID
Domain/Hinge ID
Residues
Filename_ChainID
Domain/Hinge ID
Residues

For more details on the curvilinear projection (movie) please read: LINK GOES HERE

Eigenvalues and Eigenvector indecies start from 0 (includes rigid body motion)

How many modes do you want to get a curvilinear projection (movie)? (Note: First non-rigid mode is 6.pdb; Second non-rigid mode is 67.pdb and so on)
Number of frames you want in the movies.
Scale for the movie