Profiles-3D

Contents

Release 98.0, December 1998

1. Introduction

What is Profiles-3D?

Hardware and installation

Profiles-3D environment

Location of Profiles-3D

About this book

Typographical conventions and terminology

2. Theory

Overview of 3D Profile Analysis

Determining the Residue Environment

Calculation of Area Buried and Fraction Polar

The 3D-1D Scoring Matrix

Alignment Using the Profile Method

Strategies for Using the 3D Profile Method

Normalization to Compensate for Length Effects

Interpreting the 3D-1D Score in Structure Verification

3. Application

Running Multiple Instances of the Find_Structures and Find_Sequences Commands

Using the Textport Window

Error Message Display

4. Command Summary

5. Methodology

Searching a Database of 3D Profiles

Specification of the Model Sequence

Specifying the 3D Profiles to Be Searched

Alignment Parameters

Interpretation of the Output File

Browsing and Loading Search Results

Assessment of Hypothetical Protein Structures

Information in the Textport

Graphs, Subsets and Tables Created by the Verify Command

Creating 3D Profiles

Interactive Mode Operation

Batch Mode Operation

Creating Profiles Having Position-dependent Gap Penalties

Searching Protein Sequence Databases

Specification of the Probe Profile

Specifying the Protein Sequence Databases to Be Searched

Alignment Parameters

Interpretation of the Output File

6. Tutorial

Lesson 1: Searching a Database of 3D Profiles

Lesson 2: Finding a Structural Error in a Model Protein Structure

Lesson 3: Searching Protein Sequence Databases

A. References

B. File Formats

3D-1D Scoring Table

3D Profile Files

Environment File

sphere.dat File

C. Glossary

D. seq_extract Utility

Output

Results Displayed on the Screen

Output Files

Execution Options

Index