Conformational Search and Analysis

      Contents

Release 4.5, June 2000

How to Use This Book

Who should use this book

Using other Cerius² books

Typographical conventions

1. Performing a Conformational Search

Introduction

Accessing Conformational Search

General methodology

Running a conformational search

To run a search

Defining variable torsions

To define search torsions

Setting torsion rules and classification criteria

To specify torsion rules

Setting grid scan preferences

To specify Grid Scan preferences

Setting random sampling preferences

To specify random sampling preferences

Setting Boltzmann Jump preferences

To specify the Boltzmann Jump variables

Specifying search output

To specify search preferences

Systematic search

To set up a systematic search

To perform a standard search

Energy search type

Pharmacophore search type

Setting systematic search preferences

To set torsion ranges preferences

To set ring closure bonds preferences

To set distance constraint preferences

To set duplicate removal preferences

To set scale radii preferences

Pharmacophore mapping preferences

ConFirm search

To perform a ConFirm search

Theory

Choosing a search method

Grid scan

Random sampling

Boltzmann jump

2. Performing a Conformational Analysis

Introduction

Accessing Conformer Analysis

General Methodology

Selecting a search file for analysis

To select the search file to be analyzed

Processing conformations

To perform conformation processing

Displaying conformations

Displaying a single conformation

Overlaying conformations

To overlay conformations

Matching conformation geometry

To match conformation geometry

Using a reference conformation

To use a reference conformation

Selecting conformations for analysis

To select a conformation or set of conformations

Defining torsions

To define torsions for analysis

Using the Analysis table

To examine and update the table

Analyzing conformational similarities

To automatically generate conformation clusters

To manually generate clusters

To plot a profile

To Plot a distribution

To Plot correlations

3. Field Calculation

Introduction

General Methodology

Generating probe maps

Setting up the grid

Setting calculation preferences

Calculating a probe map

Saving a probe map

Visualizing probe maps

Loading a probe map

Viewing a probe map

Managing probe maps and surfaces