Help on LIGSITEcsc.

LIGSITEcsc is a web server for the automatic identification of pockets on protein surface using Connolly surface and degree of conservation!


Usage:

First brows your own pdb file or enter a PDB ID. If you enter a PDB ID, please also give the chain ID. The chain ID should be seperated by comma if more than one. If no chain ID is given, we will consider the entire structure associated with given PDB ID. Please set up the parameters and click the "Find pockets" button. Please be patient since it may take up to 1 minute depending on the size of your protein and the parameters you choose.

The parameters:

By default the grid space is 1.0 Angstrom. You choose 1.5, 2.0 as well. The bigger the grid space, the faster speed. You can set up the number of pocket sites you want. Once the pocket sites are found, you can set the radius of a sphere probe centering at the pockets to generate potential binding sites. By default it is 5.0 Angstrom. You can also re-rank these pocket sites by their degree of conservation.

The procedure:

The protein you submit is first centered at the geometric center of all atoms coordinates. Then it is oriented so that the principal components of the atoms is aligned with the XYZ axes. The protein is projected onto a 3D grid. You can set the grid space (Default is 1.0 Angstrom). The size of the grid is determined by the size of the protein. The detail algorithm of LIGSITEcsc is illustrated here. These identified pocket sites are first ranked by their number of pocket grids. You can re-rank them by their degree of conservation derived from ConSurf-HSSP database. This conservartion re-ranking only works for the structures deposited in PDB, i,e, you input a valid PDB id.

The Pocket format:

The pockets are represented using the standard PDB file format. The residue name is "PKT" which means "Pocket". The residue id is the number of grids in this cluster in descending order. By default, only the top 3 pockets are shown, you can change the number of the pockets.

    ATOM      1  Fe  PKT Z  16      -1.625  -5.500  -3.750
    ATOM      2  Fe  PKT Z   7       5.714  11.429   3.714
    ATOM      3  Fe  PKT Z   6      10.333  -1.333   6.000
    
Visualization:

If you want to visualize them in Rasmol or PyMol, choosing the "sphere" representation for the pockets and "surface" representation for your protein is a good visualization. A python script called "yourprotein.pml" is also provided for visualization using PyMOl. Just typing "pymol yourprotein.pml" will give a good visualization in PyMol.

Potential Binding sites:

To get the potential binding sites of your protein, you can set the radius of a probe which is centered at the grid coordinates. Those atoms in your protein within the sphere are selected as potential binding sites. By default the radius is 5.0 Angstrom.


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