Using 3D-SURFER

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Using 3D-SURFER
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Before you start

• 3D-Surfer can be accessed at http//dragon.bio.pur
  due.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/plugi
  n/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-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 Submit
Click on Submit to view the results of the query
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Upload your own PDB file ...
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File Upload
Access 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 images produces the
animated surface displaying different
views. Click on the image to access query results
for the PDB chain
Moving the mouse over the text highlights the
clickable link to the PDB website.
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 Cavity regions
Click to identify Protrusion regions
Click to identify Flat 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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VISGRID
Largest 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