Help on metaPocket!

Help Content

1. Help on Server Usage

  • Server usage
  • PDB id
  • Chain id
  • Upload file
  •  

    2. Help on prediction result

  • Result download:
  •  

    3. Help on Jmol View Control Panel

  • Prediction Results
  • Zoom in and take a closer look
  • Take it for a spin
  • Protein visual model
  • Color settings
  • Reset to original orientation
  •  

    If you have other questions about the server please feel free to send us an e-mail and we will be very happy to get any word of you.

    1. Help on Server Usage 

    Server usage:     top

    First brows your own pdb file or enter a PDB ID, after doing this, please also select the chain ID. If no chain selected, you will be told to do it.

    If you want us to send the link of the result page to you, please also give an proper e-email address of you.

    After this, please click the "Predict" button to do prediction and please be patient since it may take up to tens of minutes depending on the size of your protein and the status of the base servers.

    Now you can take a cup of coffee or do something else, don't worry, you will get an email of the result link if you set the email address correctly.

    PDB id:     top

    The PDB id of protein in Protein Data Bank, normally it should be 4-letter length.

    Chain id:     top

    The chain id of the protein that you want this server to find interaction binding sites for you. If no chain selected, you will be told to do it.

    Upload file:     top

    MetaPPI server allow you to upload the pdb file of your own to do prediction instead of giving a PDB id. This is useful for some special use. But you also should select a chain ID for it.

     

    2. Help on prediction result 

    Result download:     top

    You can download the prediction result files here. The descriptions of all downloadable files are shown bellow:

    MetaPPI results:
    (1) The PDB format of protein you submit: this is the protein file of PDB format which is used to do prediction with.
    (2) MetaPPI result: PDB format file with prediction scores in the tempFactor field.
    (3) A python script for visualization using PyMOL: this file is used to visualize your prediction result in PyMOL.

    Base server results:
    You can download result files of all successful base servers, the format of the file will be as the same as metaPPI. And metaPPI also downloads the result page of each server, you can also open it by clicking the link of "Output Page".

     

    3. Help on Jmol View Control Panel 

    Prediction Results:     top

    Click to view full sized image !

    All results of each server will be shown in this Jmol view module. You can click one of the radio button to show the result of the corresponding server.

    Residues in protein will be shown in different colors, different color stands for different prediction scores. Please see the following image:

    In the image above, scores of colors will be higher from left to right.

    Zoom in and take a closer look:     top

    If you find the graphic in the viwe panel is too small to look, you may zoom in and take a closer look by choosing a button to click, a user may zoom in the view as 100%, 300% and 500%.

    Take it for a spin:     top

    Take the view panel for a spin, spin the view panel to see the structue of pockets and protein.

    Protein visual model:     top

    You can choose to make the Jmol view show the protein structure in different models:
    (1) ball-and-stick:  show protein structure in ball and stick model.
    (2) trace:  show the trace of protein structure.
    (3) cartoons:  show protein structure in cartoon model.
    (4) wireframe:  show protein structure in wireframe model.
    (5) spacefill:  show protein structure in ball model only, and allow you
    control the spacefill of the atom ball.
    (6) backbone:  show backbone of protein structure.

    Color settings:     top

    You can choose to color 6 regions of the view in different colors:
    (1) background:  color the background of the view.
    (2) overall:  color the whole part of the view except the background.
    (3) protein:  only color the protein structure of the view.

    Reset to original orientation:     top

    Make the view panel show the pockets and protein structure in the original orientation. This is useful when you changed the orientation of the view and want it to back.

     

    --> Home Page <--

     

     

    If this server is useful for your work, please cite:

    Bingding Huang and Michael Schroeder(2008), Using protein binding site to improve protein-protein docking Gene, Epub 1;422(1-2):14-21. <Link>

    Contact us

    Bingding Huang(Project leader), Email: bhuang@biotec.tu-dresden.de
    Zengming Zhang, Email: zmzhang@mail.systemsbiozju.org
    Jingna Si, Email: jingna@mail.systemsbiozju.org
    Wenhan Wang, Email: glwenhan@gmail.com

    Report Bugs

    If you find some bugs of this server, please help us improve it by reporting bugs to <Zengming Zhang>, any help from you will be greatly appreciated!

    Acknowledgement

    Funding from MOST China (grant no: 2008DFA11320) and EU 7th Framework Marie Curie Actions IRSES project (grant no: 247097) is acknowledged! Imprint.