Using 3D-SURFER

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/

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

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)

Input a PDB chain

Select a Protein chain

Enter the protein PDB code followed by the chain ID (if any). Format “####-#”

Select a Protein chain

A pop up menu assists in the selection of the protein

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

Select a Protein chain

Click on “Submit” to view the results of the query

Click Submit

Upload your own PDB file ...

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.

The Results Page

An overview of the Results page

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.

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

Visualizing Alignments

Click on the “Rmsd” button to view the CE based

structural alignment

RMSD between structures as calculated by the CE program

Analyzing local geometric features using VISGRID

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.

VISGRIDLargest Cavity

2nd Largest Cavity

3rd Largest Cavity

Surface area and volume of the convex hull formed by the atoms of the listed residues

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

Thank you for using 3D-SURFER