Subject: FRED 2.0 released - extremely fast, exhaustive ligand docking in a protein active site

From: George Vacek <vacek/at/eyesopen.com>
Date: Wed, 10 Nov 2004 09:59:17 -0700

OpenEye has released FRED 2.0, an accurate and extremely fast docking 
program. For every ligand, FRED exhaustively searches all possible poses 
within a protein active site, filtering for shape complementarity and 
optional pharmacaphoric features before being evaluated by several 
scoring functions (ChemScore, PLP, ScreenScore, ChemGauss, PBSA).

Whereas most docking codes use stochastic methods to find binding modes, 
FRED uses a systematic search algorithm, accurately predicting binding 
modes in a reproducible manner. Furthermore, FRED allows the scientist 
to take advantage of known structure activity relationships; they may 
perform directed docking wherein certain pharmacaphoric features are 
guaranteed to be in specific regions of the active site. Despite being 
exhaustive, FRED is extremely fast; distributed processing via PVM docks 
even the largest libraries in reasonable time frames. With equivalent 
resolution settings, FRED will out-perform all competitive methods.

FRED 2.0 has two new, more accurate, scoring functions: ChemGauss adds 
chemical perception to the original shape-based function; PBSA provides 
Poisson-Boltzman electrostatic binding energies. FRED 2.0 is capable of 
refining docked structures in the context of the active site using the 
high-quality Merck Molecular Force Field (MMFF). For consensus scoring, 
FRED 2.0 supports multiple simultaneous scoring functions and hit lists. 
To eliminate promiscuous binders, FRED 2.0 can scale scoring results 
based upon Multiple Active Site Corrections.

For further information, please visit www.eyesopen.com or contact
business/at/eyesopen.com.

Regards,
George Vacek
VP, Business Development
OpenEye Scientific Software