Posted by: shrikantmantri | October 24, 2009

3D-SURFER: software for high-throughput protein surface comparison and analysis

via Bioinformatics – current issue by La, D., Esquivel-Rodriguez, J., Venkatraman, V., Li, B., Sael, L., Ueng, S., Ahrendt, S., Kihara, D. on 10/23/09

Summary: We present 3D-SURFER, a web-based tool designed to facilitate high-throughput comparison and characterization of proteins based on their surface shape. As each protein is effectively represented by a vector of 3D Zernike descriptors, comparison times for a query protein against the entire PDB take, on an average, only a couple of seconds. The web interface has been designed to be as interactive as possible with displays showing animated protein rotations, CATH codes and structural alignments using the CE program. In addition, geometrically interesting local features of the protein surface, such as pockets that often correspond to ligand binding sites as well as protrusions and flat regions can also be identified and visualized.

Availability: 3D-SURFER is a web application that can be freely accessed from:


Supplementary information: Supplementary data are available at Bioinformatics online.

Posted via email from Sharing significant bytes —(Shrikant Mantri)


Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )


Connecting to %s


%d bloggers like this: