3D-Dock Suite

http://www.bmm.icnet.uk/docking/

3D-Dock Suite

Incorporating

FTDock, RPScore and MultiDock

Introduction

The growing number of individual protein structures in the databases and the relatively small number of solved complexes makes predictive docking an important theoretical method. 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. FTDock implements the Fourier correlation algorithm of Katchalski-Katzirand coworkers plus an electrostatics function amenable to Fourier correlation that was developed in this laboratory.

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. This program is fully integrated with the present version of FTDock.

A further improvement in the quality of the predictions can be gained by using MultiDock (Multiple copy side-chain refinement Dock ).

We have tested the combined algorithms on over a dozen protein-protein systems with good results. Developers of docking algorithms may be interested in our decoy sets, which are available through the systems page.

All software is available for download.

Versions History

The original version (1.0) of FTDock was written in 1997 by Henry Gabb. It was written in Fortran 77 with parallel capabilities for a Silicon Graphics Challenge machine. It was used for the CASP2 conference with some success.

The present version (2.0) of FTDock was written by Gidon Moont. It is written in C, with no parallel capabilities at present. A primary reason for rewriting was portability. The Fourier library now used is FFTW ( Fastest FourierTransform in the West ), which is gnu licensed and portable to most platforms. The other reason was to enable RPScore (also written by Gidon Moont) to be able to handle the output in a more integrated manner.

MultiDock was written by Richard Jackson. It is written in Fortran 77, and is currently only available as an executable for either the Silicon Graphics IRIX enviroment or for Linux (i386). It was used for the CASP2 in conjunction with version 1.0 of FTDock.

In between major version updates, minor maintance updates will be made continually. These are Documented on thedownload page.

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