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Using 3D-SURFER
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Before you start
3D-Surfer can be accessed at http://dragon.bio.purdue.edu/3d-surfer
For visualization of results, 3D-Surfer requires a Java enabled browser. The Java plugin can be downloaded from http://java.sun.com/products/plugin/downloads/
The Jmol package is used for visualizing protein structures. Jmol tutorials can be accessed from http://jmol.sourceforge.net/docs/
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About 3D-Surfer
3D-SURFER3D-SURFER is a web based tool for protein surface comparison and analysis
Rapid comparison of protein structures is enabled by the use of 3D Zernike moment invariants (Novotni and Klein, 2004)
The server is easy to use. The only input is a PDB ID followed by a chain (if any).
Read on to see what 3D-Surfer can do
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3D-Surfer Functionality
Search and retrieve PDB structures that have similar surface shapes based on the Euclidean distance between the descriptor vectors representing the proteins
Results displayed include
CATH codes that reflect the structural topology
Alignments based on CE can also be viewed at the click of a button
View local geometric features of interest using VISGRID
Zernike Invariants of each protein (text and graph)
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Input a PDB chain
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Select a Protein chain
Enter the protein PDB code followed by the chain ID (if any). Format “####-#”
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Select a Protein chain
A pop up menu assists in the selection of the protein
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Select a Protein chain
Optionally, change the filtering settings. CATH filtering, hits with equal CATH codes, while
residue length filtering only displays matches that are similar in length to the query structure
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Select a Protein chain
Click on “Submit” to view the results of the query
Click Submit
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Upload your own PDB file ...
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File UploadAccess the “Upload”
page
Select the PDB file to be processed by uploading a structure using the “Browse” button. Add the chain ID (if any). Click on “Submit” to view the results.
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The Results Page
An overview of the Results page
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Listing Results
Results o f the query may saved separately by clicking on the “List Results” button.
The user may also select the number of entries (default 25) to be listed.
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Results
Moving the mouse over the text highlights the clickable link to the PDB website.
Moving the mouse over the images produces the animated surface displaying different views.Click on the image to access query results for the PDB chain
Euclidean distance between the Zernike moments of the query protein and 1CI1-A
Select the Check box to calculate the RMSD between the query protein and 1CI1 using CE. See the next slide for details
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Visualizing Alignments
Click on the “Rmsd” button to view the CE based
structural alignment
RMSD between structures as calculated by the CE program
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Analyzing local geometric features using VISGRID
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VISGRID
Click to identify CavityCavity regions
Click to identify ProtrusionProtrusion regions
Click to identify FlatFlat regions
Visualize the results in terms of the list of the residues forming of the three largest groups. Areas and volumes for these regions are also reported.
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VISGRIDLargest Cavity
2nd Largest Cavity
3rd Largest Cavity
Surface area and volume of the convex hull formed by the atoms of the listed residues
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Other links
Documentation - About 3D-SURFER
FAQ - Definitions of terminology and other questions on using 3D-SURFER
Please help us improve the website by sending your comments and suggestions. Access our list of contacts at http://dragon.bio.purdue.edu/3d-surfer/index.php?contact
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Thank you for using 3D-SURFER