AFPredictor – Predicts potential Ice-binding Sites based on Geometric Analysis of the Protein Surface

AFPredictor

:: 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

DoxeyLab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb Server

:: 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.

VisGrid – Identify Pockets in Protein Surfaces

VisGrid

:: 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

  • Linux

:: DOWNLOAD

 VisGrid

:: 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.

3D-SURFER 2.0 – Real-time Search and Characterization of Protein Surfaces

3D-SURFER 2.0

:: 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

  • Web browser

:: 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.

PFP 2.3 – Extracting and Displaying Positive Electrostatic Patches on Protein Surfaces

PFP 2.3

:: 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

  • Web Browser

:: 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.

EPOS_BP 1.0 – Ensemble of Pockets on Protein Surfaces with BALLPass

EPOS_BP 1.0

:: DESCRIPTION

EPOSBP – Ensemble of Pockets on Protein Surfaces with BALLPass

::DEVELOPER

Chair of Computational Biology at the Saarland University

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Linux
  • Ball

:: DOWNLOAD

 EPOSBP

:: MORE INFORMATION

MSPocket 1.1 – Detection and Graphical Analysis of Protein Surface Pockets

MSPocket 1.1

:: DESCRIPTION

MSPocket is an orientation independent program for the detection and graphical analysis of protein surface pockets.

::DEVELOPER

Zhu, Hongbo.

:: SCREENSHOTS

MSPocket

:: REQUIREMENTS

  • Linux / Windows /Mac OsX
  • Python
  • Biopython
  • MSMS
  • PyMOL

:: DOWNLOAD

 MSPocket

:: 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.