Structure Based Focusing

Contents

Release 4.5, June 2000

1. Introduction

2. Theory

Interaction site generation

Rules governing the generation of interaction sites

H-donor and H-acceptor rules

Hydrophobic contacts rules

Summary of rules

Scoring Function

3. Methodology

The basic methodology

The interface

Define Active Site control panel

Defining the active site

Active Site Viewer control panel

Query Builder control panel

Building a query (brief description)

Building a query (detailed description)

Edit Interactions control panel

Cluster Interactions

Edit Clusters

Display

Generate Volume Exclusions

Single vs. multiple queries

General options for query generation

Options for multiple query generation

Build Query

Library focusing

Catalyst

Generate 3D virtual library

Screen virtual library

Compute Ludi Score

Hitlist Browser

4. Tutorials

Description of the lessons in this chapter

Access to the lessons as log files

Lesson 1: a single query database search

Lesson 2: generating a query from existing models

Lesson 3: multiple query database search (trypsin)

Lesson 4: multiple query database search (HIV protease)

A. References