Cerius2 Hypothesis and Receptor Models

Contents

Release 4.5, June 2000

How to Use This Book

Preparing to work

How to find information

Using other Cerius2 books

Typographical conventions

1. Introduction to C2·Hypothesis and Receptor Models

Understanding the modules

Before you begin

Accessing C2 modules

2. Aligning Models

Aligning models using field alignment

Aligning models using Moments alignment

Alignment of non-rigid models

Multiple model alignment strategies

RMS alignment

3. Incorporating Align Data in QSAR

Preparing models for generating alignment similarity descriptors

Adding alignment similarity descriptors to the QSAR Study Table

Using the study table to analyze a consensus alignment

Using alignment similarity descriptors for QSAR analysis

Recalculating alignment similarity descriptors

4. Theory: Alignment

Model Alignment Strategies and Methods

RMS Superposition

Electrostatic Potential Similarity

Steric Shape Similarity

Field Alignment (Electrostatic & Steric Similarity)

Steric Clash (Bump) Checking

Implementation: Gaussian Approximation of Overlap Functions

PART 2: Receptor

5. Introduction to Receptor

Accessing Receptor

Using Receptor

6. Receptor QuickStart

QuickStart

7. Tutorial: Receptor Surface Analysis (RSA)

Before you begin

Load Models and add them to the Study Table

Generate a Receptor Surface Model (RSM)

Add Receptor Surface energies to the Study Table.

Calculate a QSAR

8. Generating a Receptor Model

Generating a receptor surface model

Setting preferences

Saving and restoring a receptor model

Listing a receptor model

Mapping property values

9. Evaluating Structures Against a Receptor Model

Evaluating structures

Setting preferences

Viewing the results

Incorporating receptor data in QSARs

Building a QSAR using receptor data

Using a QSAR with receptor data to estimate activity of a structure

10. Theory: Receptor Models

Receptor surface models

Mapping properties

Molecule-Receptor model interactions

RSA (Receptor Surface Analysis)

11. Introduction to Generating a Pharmacophoric Hypothesis

Using ConFirm and HipHop

12. Generating Conformations

Running ConFirm

13. Generating and Using Alignment Hypotheses

Aligning common molecular features

Setting preferences using the Preferences control panel

Incorporating activity data into a hypothesis

Using aligned structures to generate receptor models

PART 4: Database Query

14. Performing a Database Query

Available database searches

Preparing to work with Database Query

Methodology

Constructing a query

Constructing an atom query

Constructing a bond query

Constructing a centroid query

Constructing a distance query

Deleting all query features

Submitting a query

Submitting a Catalyst query

Submitting a SHAPE query

Submitting an ISIS query

Defining a Database Domain from Prior Query Hit List

Retrieving and browsing database hits

Manipulating a hit list

A. References