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.

"""
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.
"""

Did you find this post helpful?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Structure-based prediction of methyl chemical shifts in proteins Structure-based prediction of methyl chemical shifts in proteins Abstract Protein methyl groups have recently been the subject of much attention in NMR spectroscopy because of the opportunities that they provide to obtain information about the structure and dynamics of proteins and protein complexes. With the advent of selective labeling schemes, methyl groups are particularly interesting in the context of chemical shift based protein structure determination, an approach that to date has exploited primarily the mapping between protein structures and backbone chemical shifts. In order to...	nmrlearner	Journal club	0	07-15-2011 09:10 PM
[NMR tweet] http://www.pulist.net/field-guide-to-spectroscopy-spie-vol-fg08.html #nuclear #magnetic #resonance #approximation Field Guide to Spectro http://www.pulist.net/field-guide-to-spectroscopy-spie-vol-fg08.html #nuclear #magnetic #resonance #approximation Field Guide to Spectro Published by pubooks (Joel Michal) on 2011-03-10T12:44:15Z Source: Twitter	nmrlearner	Twitter NMR	0	03-10-2011 12:52 PM
Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Related Articles Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction. Structure. 2010 Dec 8;18(12):1678-1687 Authors: Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ Protein-biomineral interactions are paramount to materials production in biology, including the mineral phase of hard tissue. Unfortunately, the...	nmrlearner	Journal club	0	12-08-2010 06:21 PM
[NMR paper] TOUCHSTONEX: protein structure prediction with sparse NMR data. TOUCHSTONEX: protein structure prediction with sparse NMR data. Related Articles TOUCHSTONEX: protein structure prediction with sparse NMR data. Proteins. 2003 Nov 1;53(2):290-306 Authors: Li W, Zhang Y, Kihara D, Huang YJ, Zheng D, Montelione GT, Kolinski A, Skolnick J TOUCHSTONEX, a new method for folding proteins that uses a small number of long-range contact restraints derived from NMR experimental NOE (nuclear Overhauser enhancement) data, is described. The method employs a new lattice-based, reduced model of proteins that explicitly...	nmrlearner	Journal club	0	11-24-2010 09:16 PM
Protein secondary structure prediction using NMR chemical shift data. Protein secondary structure prediction using NMR chemical shift data. Related Articles Protein secondary structure prediction using NMR chemical shift data. J Bioinform Comput Biol. 2010 Oct;8(5):867-84 Authors: Zhao Y, Alipanahi B, Li SC, Li M Accurate determination of protein secondary structure from the chemical shift information is a key step for NMR tertiary structure determination. Relatively few work has been done on this subject. There needs to be a systematic investigation of algorithms that are (a) robust for large datasets; (b)...	nmrlearner	Journal club	0	10-29-2010 07:05 PM
[BMNRC community] The PSIPRED Protein Structure Prediction Server The PSIPRED Protein Structure Prediction Server http://bioinf.cs.ucl.ac.uk/psipred/ Go to BMNRC community to find more info about this topic.	nmrlearner	News from other NMR forums	0	09-04-2010 06:53 AM
Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff Computational prediction of three-dimensional protein structure from NMR chemical shifts - Kai Kohlhoff, Microsoft Research Summer School, Cambridge, July 2008	MCGowan	Educational web pages	0	09-16-2008 02:10 AM
Prediction of binding sites from protein structure Surfnet http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html	nmrlearner	A test forum	0	09-19-2005 05:54 AM

« Previous Thread | Next Thread »

Posting Rules
You may not post new threads You may not post replies You may not post attachments You may not edit your posts BB code is On Smilies are On [IMG] code is On HTML code is On Trackbacks are Off Pingbacks are Off Refbacks are Off