We have developed a platform - FORECASTER - that includes our unique and highly accurate programs for drug discovery and process chemistry:
1. FITTED, a docking program 2. PREPARE, PROCESS and SMART, programs that can prepare protein and ligand files automatically 3. SELECT, a program that computes compound similarity, extracts focused highly diverse libraries or identifies analogues 4. FILTER, a program that filters using descriptors and functionnal groups 5. REACTOR, a program that performs combinatorial chemistry in silico from user-defined chemical schemes 6. ACE, a program that predicts the stereochemical outcome of reactions
Release of FITTED 3.0
The new version 3.0 of the FITTED Suite is now available for download.
Overview:
FITTED is a suite of programs to dock flexible ligands into flexible proteins. This software relies on a genetic algorithm to account for flexibility of the two molecules and location of water molecules, and on a novel application of a switching function to retain or displace water molecules and to form potential covalent bonds with the protein side-chains.
The Suite includes many new features and implementations:
FITTED is a suite of programs (FITTED, PREPARE, ProCESS and SMART)
GUI for easy keyword file editing and docking
Fully automated and flexible docking program
No more complex directory architecture required
Multi-mol2 support for docking and ligand processing
Uses an evolutionary algorithm
Semi-flexible protein docking with flexible waters
Has the ability to consider water molecules displaceable
Keyword files are simpler than ever
New installation script (Linux, Mac OSX)
Program files located in a system directory
Support for Windows, Linux 32 and 64 bits, Mac OSX.
Major changes and new usage
FITTED:
New Scoring Function RankScore5 (best for virtual scoring)
Improved matching algorithm for better initial populaiton
Faster code execution for quicker docking runs
Support for multi-mol2 file for docking multiple molecules
Different docking modes available: Dock, SAR, and Local
PREPARE:
New program PREPARE for easy preparation of pdb structure
Adds hydrogens
Optimizes tautomers and water molecules
Generates protonation states
Reconstructs missing side chains using a conformational library
SMART:
Keywork file is now required
Reads mol2 and sdf (3D format) as single or multi mol files
Outputs mol2 as single or multi mol files
Assigns partial charges using either MMFF or DGH (Electronegativity equalization-derived) models
Assigns descriptors for filtering via bit strings
ProCESS:
Improvement of compatibility with protein structures
Improved interaction site definition
Validation:
Successful and accurate docking of various enzyme inhibitors (i.e., HIV-1 protease, trypsin, MMPs, mannosidase), receptor agonists and antagonists (glutamate receptor) and virtual screening of enzyme inhibitors (i.e., CDK2, thymidine kinase, HCV polymerase) receptor agonists and antagonists (estrogen receptor). Read more about FITTED
ProCESS is a module used in the preparation of the protein input files for FITTED. ProCESS (i) can truncate the protein to reduce its structure strictly to the binding site; (ii) assigns atom types and partial charges; (iii) checks the protein files for consistency if more than one is used; (iv) precomputes the atomic solvation data; (v) identifies the binding site cavity and the interaction sites and prepares the files describing them.
