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Bioinformatics Advance Access published online on February 28, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn062
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ISD: A software package for Bayesian NMR structure calculation

Wolfgang Rieping 1,*, Michael Nilges 2 and Michael Habeck 3,*

1Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK. 2 Unité de Bioinformatique Structurale, Institut Pasteur, Centre National de la Recherche URA 2185, 25-28, Rue du Dr Roux, 75724 Paris Cedex 15, France. 3 Max Planck Institute for Developmental Biology, Spemannstrasse 35 and Max Planck Institute for Biological Cybernetics, Spemannstrasse 38, 72076 Tübingen, Germany.

*To whom correspondence should be addressed. Dr Wolfgang Rieping, E-mail: wolfgang.rieping{at}bioc.cam.ac.uk


  Abstract

Summary: The conventional approach to calculating biomolecular structures from nuclear magnetic resonance (NMR) data is often viewed as subjective due to its dependence on rules of thumb for deriving geometric constraints and suitable values for theory parameters from noisy experimental data. As a result, it can be difficult to judge the precision of an NMR structure in an objective manner. The Inferential Structure Determination (ISD) framework, which has been introduced recently, addresses this problem by using Bayesian inference to derive a probability distribution that represents both the unknown structure and its uncertainty. It also determines additional unknowns, such as theory parameters, that normally need be chosen empirically. Here we give an overview of the ISD software package, which implements this methodology.

Availability:The program is available at http://www.bioc.cam.ac.uk/isd.

Contact: wolfgang.rieping{at}bioc.cam.ac.uk, michael.habeck{at}mpg.tuebingen.de

Associate Editor: Prof. Alfonso Valencia

Received on September 3, 2007; revised on February 12, 2008; accepted on February 16, 2008

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