A Guide to Structure Prediction, by Rob Russell
 

A Guide to Structure Prediction (version 2.1) (link)

Rob Russel (for EMBL) gives a useful, step-by-step guide to predicting 3D protein structure, and provides links to numerous online resources. An excerpt from the website is pasted below.

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Introduction

This is by no means intended to be a comprehensive guide to predicting protein 3D structure. Rather, I have tried as best as possible to summarise my general approach to the problem in a manner that I hope is useful and not too difficult to follow. I apologise in advance for failing to include various references, WWW sites, etc. I would strongly recommend exploring the WWW pages given here, and looking for "related sites", etc. In this way you should get a more comprehensive picture of what is available.

The assumption is that you have a sequence of a protein that you want to know more about. Before you start, remember that this approach will not always provide satisfying or complete answers. However, it is increasingly rare that the techniques described here fail to shed any light on a protein sequence. Just a little time to analyse a sequence can possibly save time and money by aiding experimental design.

I should emphasise that the title of talk for the above meeting was Secondary structure prediction and fold recognition. The contents of these pages are thus heavily biased towards these two subjects (e.g. there are no figures for most of the other sections). Mostly, however, there are links within the other sections that can give you more information about them.
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