QUANTUM 3.1

© 2005 Quantum Pharmaceuticals. All rights reserved.

Description of the Main Features of Quantum's Visualization Tools

Description of Drug Discovery Tools

Comparative analysis of Quantum's calculations and experimental data

Description of the Main Features of Quantum's Visualization Tools

Introduction

About this User Manual

Software/Hardware requirements

Installation

Quantum's Windows

Getting Started

Loading a Molecule

Changing the View

Exploring Different Drawing Styles

Exploring Different Actions, Labeling and Coloring Methods

Selections

Selecting Controls

Sequence Viewer Button

Selecting using the Main Menu

Moving and Building Molecules

General Information

Moving a Molecule or Its Parts

Building Molecules

Another Useful Features

Ray-Tracing and Saving images

Labels

Distance

H-bonds and Polar Contacts

Description of Drug Discovery Tools

General Information

The IC50 of a Protein-Ligand Complex

Selecting a Ligand

Setting the Protonation State and Adding Explicit Hydrogen Atoms to the Ligand

Selecting Other Structures Near the Ligand (if any)

Adding Hydrogen Atoms to the Protein and to the Hetatoms

Calculations and Results

Ligand Docking

Selecting a Small Molecule for Docking

Setting the Protonation State and Adding Explicit Hydrogen atoms to the Ligand

Building a Grid box in the Active Site

Selecting Essential Metal Ions and Hetatoms in the Active Site

Adding hydrogen atoms to the protein and to the hetatoms

Calculations and Results

Library Screening

Create and Open a Library

Building a Grid Box in the Active Site

Selecting Essential Metal Ions and Hetatoms in the Active Site

Calculations and Results

The IC50 of a Protein-Protein Complex

Selecting Proteins

Selecting Essential Metal Ions and Hetatoms in the Active Site (if any)

Adding hydrogen atoms to the proteins and to the hetatoms

Calculations and Results

Large-Scale Protein Movements

Selecting Protein

Building a Box

Results of the Procedure

ProteinSpectrumScreen

Opening a Library

Selecting Proteins

Screening Results

Mutagenesis

Mutations

After pushing the binding activity button, the procedure offers the following steps:

Setting the protonation state and adding explicit hydrogen atoms to the ligand

Selecting other structures near the ligand (if any)

Adding Hydrogen Atoms to the Protein and to the Hetatoms

Results of the Binding Activity Change

Rational Drug Design

Quantum's Algorithm

Select a Protein

Building a Grid Box in the Active Site

Selecting Essential Metal Ions and Hetatoms in the Active Site

Adding hydrogen atoms to the protein and to the hetatoms

Calculations and Results

Solubility

Select a molecule or a library

Set solvent

Results

Model Build

Select molecule/atoms

Set parameters

Superimpose

Selecting Molecules and Setting Parameters

Results of Fitting