New Features / Improvements¶
Optional GUI setup and preparation of the active site (the actual docking remains command line). The GUI allows users to
Separate bound ligands and solvent molecules from the protein structure.
Detect active sites, and adjust the box defining the active site.
Manually tweak residue protonation states.
Visualize and adjust the complimentary shapes FRED uses during the exhaustive search.
A new version of the Chemgauss scoring function, version 3, which includes new desolvation terms as well as improved typing.
Ligand based design scoring functions, C.G.O (Chemical Gaussian Overlay) and C.G.T. (Chemical Gaussian Tanimoto). These functions score be measuring how well a molecules shape and chemistry overlay a known bound ligand placed in the active site.
All new algorithm for generating the negative image of the active site using molecular shape probes, as opposed to the atomic probes uses earlier.
On the fly preparation of MASC data for runs using the MASC variant scoring functions is now an option. Pre-calculating MASC data is still available and most efficient when doing multiple runs.
FRED now uses a special receptor file to describe the active site. This file can be created interactively using the new fred_receptor GUI program, or on the fly with the command line using the same flags as the previous version of FRED (2.1.x).
The functionality of the masc_prep and ligand_info programs distributed with the previous version (2.1.x) have been merged into the main fred executable.
Version 1 of Chemgauss has been removed, Version 2 is deprecated but still available.
Individual hitlist -size and -cut flags have be replaced by a single -hitlist_size flag.