x3Disorder – Determination of Three-dimensional Structure of Protein Molecules

x3Disorder

:: DESCRIPTION

x3Disorder is a tool designed for biologists that attempt to determine the three-dimensional structure of protein molecules.

::DEVELOPER

M24 – Bioinformatics Group – University of Liege

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

On the encoding of proteins for disordered regions prediction.
Becker J, Maes F, Wehenkel L.
PLoS One. 2013 Dec 16;8(12):e82252. doi: 10.1371/journal.pone.0082252.

x3CysBridges – Determination of Three-dimensional Structure of Protein Molecules

x3CysBridges

:: DESCRIPTION

x3CysBridges is a tool designed for biologists that attempt to determine the three-dimensional structure of protein molecules.

::DEVELOPER

M24 – Bioinformatics Group – University of Liege

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013;8(2):e56621. doi: 10.1371/journal.pone.0056621. Epub 2013 Feb 15.
On the relevance of sophisticated structural annotations for disulfide connectivity pattern prediction.
Becker J1, Maes F, Wehenkel L.

MOSBY 0.955 – View Atomic Structures of Protein Molecules

MOSBY 0.955

:: DESCRIPTION

MOSBY ((MOlecular Structure Browser with analYsis)) is a program to view atomic structures of protein molecules. Beyond its basic molecular graphics functions, extension modules provides custom functions for research works in structural biology and computational molecular biology.

::DEVELOPER

Yutaka Ueno, AIST Tsukuba

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux
  • C++ compiler

:: DOWNLOAD

 MOSBY

:: MORE INFORMATION

Citation

Ueno Y, Asai K.
MOSBY: a molecular structure viewer program with portability and extensibility.
J Mol Graph Model. 2002 Mar;20(5):411-3.

FTDock 2.0/ RPScore /MultiDock 1.0 – Protein Molecule 3D-Dock Suite

FTDock 2.0/ RPScore /MultiDock 1.0

:: DESCRIPTION

FTDock ( Fourier Transform Dock ) performs rigid-body docking on two biomolecules in order to predict their correct binding geometry. FTDock outputs multiple predictions that can be screened using biochemical information.

RPScore ( Residue level Pair potential Score ) uses a single distance constraint empiricaly derived pair potential to screen the ouptut from FTDock. It has been shown that this can reduce dramatically the list of possible complexes within which can be found a correct solution.

MultiDock (Multiple copy side-chain refinement Dock ) was developed to provide a method for refining the interface between two proteins at the atomic level given an initial docked complex generated by a docking algorithm or manual docking procedure. The motivation for this work was to provide a rapid energy refinement protocol for the large number of putative docked complexes produced by rigid-body docking programs such as FTDock or DOCK. The program models the effects of side-chain conformational change and the rigid-body movement of the interacting proteins during refinement.

::DEVELOPER

Structural Bioinformatics Group – Imperial college London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

FTDock / RPScore /MultiDock

:: MORE INFORMATION

Citation