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Introduction
Quantum
is a software package designed for the early stages of drug discovery: target
identification, drug hit identification and drug lead optimization.
Quantum's
computational platform is based on direct modeling of interactions between
molecules in biochemical processes. Advanced methods of quantum and molecular
physics were applied to calculate the energy of interactions between organic
substances. Thermodynamic values such as IC50 and Kd are final results of
modeling and allow researchers to analyze pharmacodynamic properties of drug
candidates. These simulation models are controlled by a graphic user interface,
which is used to load and modify 3D molecules and set important parameters of
the model. Quantum can be run both on parallel clusters and a workstation.
Protein
large-scale optimization, protein movement and changes in bioactivity after mutations were especially focused on.
Quantum's
toxic
side effects and compound profiling tools screen hundreds of proteins and
produce special selectivity reports for drug candidates.
These simulation models are controlled
by a graphic user interface, which is used to load and modify 3D molecules and
set important parameters of the model. Quantum can be run both on parallel
clusters and a workstation.
About
this User Manual
The
Quantum User Manual is organized into three main sections:
·
Description of the main
features of Quantum's visualization tools
·
Detailed description of drug
discovery tools
·
Comparative analysis of Quantum's
calculations and experimental data, which can be confirmed by any Quantum user
Note: Due to
the modular structure of Quantum, the functionality of the program depends on
the license you purchased. This manual describes all possible functions, and
some of them may not be accessible in your installation.
Software/Hardware
requirements
OS: Linux-32/64-bit Intel compatible CPU, glibc
>2.3; Windows 2000, Windows XP
Processsor: Pentium III, 500 MHz or better
Installation
Windows
To start the automatic installation
of Quantum:
·
Insert the program CD into the
CD-ROM drive of your computer;
·
The installer program of Quantum
automatically starts after a few seconds. If this is not the case, start the program
Setup.exe from Windows Explorer.
·
Follow the instructions of the
installation program.
· After the installation is successfully completed, the new program group
Quantum will be added to the Windows Start Menu. The Quantum Icon will be added to the Desktop.
Linux
Download the executable file,
execute and follow the onscreen instructions.
Quantum's Windows
Quantum starts with two windows
(Figure 1), which consist of:
·
the Main Menu (a) -
functions for controlling the program;
·
the Info Panel (b) - provides
the information about the current procedures of the program;
·
the Command Panel (c) - for
Quantum's commands;
·
the Viewer Window (d) - 3D
images of molecules;
·
the Viewer Menu (e) -
functions for controlling loaded molecules, selections, etc.;
·
the Names Panel (f) - the
names of the molecules, the selections, etc.
·
the Selecting Controls (g) -
the type of selection (atom, residue, molecule, etc.);
·
the Movie Controls (h) -
options for showing a movie; and
·
the Sequence Viewer button
(i) - provides with the 1D molecular structure.
Figure1-Quantum's
Windows
