:: DESCRIPTION
MSPocket is an orientation independent program for the detection and graphical analysis of protein surface pockets.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhu H, Pisabarro MT.
MSPocket: an orientation-independent algorithm for the detection of ligand binding pockets.
Bioinformatics. 2011 Feb 1;27(3):351-8.
:: DESCRIPTION
PFP or PFplus / PatchFinderPlus is a web-based tool for extracting and displaying continuous electrostatic positive patches on protein surfaces. The input required for PFplus is either a four letter PDB code or a protein coordinate file in PDB format, provided by the user. PFplus computes the continuum electrostatics potential and extracts the largest positive patch for each protein chain in the PDB file.
::DEVELOPER
Mandel-Gutfreund Lab, at the Technion.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Shula Shazman, Gershon Celniker, Omer Haber, Fabian Glaser, Yael Mandel-Gutfreund (2007)
Patch Finder Plus (PFplus): A web server for extracting and displaying positive electrostatic patches on protein surfaces.
Nucleic Acids Res., 35:526-30.
:: DESCRIPTION
Given a protein structure (PDB file), AFPredictor will predict potential ice-binding sites based on geometric analysis of the protein surface. It can be used to predict novel antifreeze proteins from 3D structure alone.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Doxey AC, Yaish MW, Griffith M, McConkey BJ. (2006)
Ordered surface carbons distinguish antifreeze proteins and their ice-binding regions.
Nature Biotechnology, 24:852-5.
:: DESCRIPTION
EPOSBP – Ensemble of Pockets on Protein Surfaces with BALLPass
::DEVELOPER
Chair of Computational Biology at the Saarland University
:: SCREENSHOTS
n/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
3D-SURFER is a web-based tool for real-time protein surface comparison and analysis. The server integrates a repertoire of methods to assist in high throughput screening and visualization of protein surface comparisons.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
3D-SURFER 2.0: web platform for real-time search and characterization of protein surfaces.
Xiong Y, Esquivel-Rodriguez J, Sael L, Kihara D.
Methods Mol Biol. 2014;1137:105-17. doi: 10.1007/978-1-4939-0366-5_8.
:: DESCRIPTION
The VisGrid algorithm identifies geometric features of protein surfaces using an intuitive concept of the visibility.
::DEVELOPER
Kihara Bioinformatics Laboratory
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Characterization of local geometry of protein surfaces with the visibility criterion.
Li B, Turuvekere S, Agrawal M, La D, Ramani K, Kihara D.
Proteins. 2008 May 1;71(2):670-83.