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Calculation Request
CASTp Information
 
About CASTp
Background
Input & output
Examples
Publications
PyMOL plugin
   
Calculation request Options
 
You can either:

  • Enter the 4 letter PDB id of the structure.
  • Upload a molecular structure in standard PDB format.

    No multiple NMR structures please, and all nonpolar H atoms will be ignored

  • Type the 4 letter pdb ID:


    Select a local file in PDB format to upload:

    Jmol - Jmol is a free, open source molecule viewer. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. It only requires that you have a Java enabled browser.
    Chime Plugin - Chime is a broswer plugin that runs under Windows, MacOS, and IRIX. This is the best choice for Windows 95/98/NT/2000/XP or IRIX. Linux user can also use this plugin by running a virtual windows environment( VMware). Chime is available from MDL's website.
    E-mail only - This option allows you to get results back via email only. No visualizations will be provided.

      E-mail results to:
    If an e-mail address is entered, the results will be sent to the given address along with the option chosen above.

    Probe radius: Angstroms.
    The default value used by CASTp server is 1.4 Angstroms. Only values between 0.0 and 10.0 will be accepted.

    Check here if you want the option to include HET groups in the calculation and/or run calculations on any combination of chains from a multiple chain structure
    Reference
    Please cite the following if you publish or present results using castP analysis:
    Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz, and Jie Liang 2006. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated resiudes.Nucleic Acid Research, 34:W116-W118.
    Additional background reading
    Jie Liang, Herbert Edelsbrunner, and Clare Woodward. 1998. Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design. Protein Sciene, 7:1884-1897.

    © 2005 All rights reserved.
    Acknowledgement
    The CASTp server is partially funded by support from National Science Foundation (DBI0078270, CAREER DBI-0133856)