Biopolymer

Contents

Release 2005, March 2005

1. Introduction

Invoking Biopolymer

Pilot tutorials

2. Protein Model Construction

Introduction

Tutorials

Background

Basics of protein structures

Hierarchy of protein structure

Methodology and implementation

Building and editing initial protein structure

Setting backbone conformation and backbone construction

Setting protein side chain rotameric states

Searching protein loop conformations

3. Nucleic Acid Model Building

Background

Methodology and implementation.

Building and extending nucleotide strands

Deleting or replacing nucleotides.

Measuring nucleotide geometric properties.

Modifying existing nucleic acid structures

4. Carbohydrate Model Building

Introduction

Tutorials

Methodology and implementation

Monosaccharide building blocks

Oligosaccharide model building

Modifying an existing carbohydrate

5. Protein Backbone Construction

Introduction

Tutorial

Theory

Methods that do not use the bond angle constraint

Methods that use the bond angle constraint

Algorithm used by the Protein/Backbone command

Accuracy

Methodology and implementation

6. Domain Analysis

Introduction

Tutorials

Methodology and Implementation

Typical task

Creation of domain clusters

Loading domain clusters

Browsing the results

Overview of commands

7. Structure Database Searching

Introduction

Tutorials

Methodology and Implementation

Searching the structural database

Defining a structure database query

Templates and constraints

Residue and secondary structure types

Restricting main chain and side chain torsions

Intra-template constraints

Inter-template constraints

Database search details

Overview of commands

A. References