Open Access
PLoS Computational Biology, volume 5, issue 3, pages e1000307
Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
1
National Magnetic Resonance Facility at Madison, Biochemistry Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America,
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2
Mathematics Department, University of Wisconsin Madison, Madison, Wisconsin, United States of America
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Publication type: Journal Article
Publication date: 2009-03-13
Journal:
PLoS Computational Biology
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 4.3
ISSN: 1553734X, 15537358
PubMed ID:
19282963
Molecular Biology
Genetics
Computational Theory and Mathematics
Cellular and Molecular Neuroscience
Ecology, Evolution, Behavior and Systematics
Ecology
Modeling and Simulation
Abstract
The process of assigning a finite set of tags or labels to a collection of observations, subject to side conditions, is notable for its computational complexity. This labeling paradigm is of theoretical and practical relevance to a wide range of biological applications, including the analysis of data from DNA microarrays, metabolomics experiments, and biomolecular nuclear magnetic resonance (NMR) spectroscopy. We present a novel algorithm, called Probabilistic Interaction Network of Evidence (PINE), that achieves robust, unsupervised probabilistic labeling of data. The computational core of PINE uses estimates of evidence derived from empirical distributions of previously observed data, along with consistency measures, to drive a fictitious system M with Hamiltonian H to a quasi-stationary state that produces probabilistic label assignments for relevant subsets of the data. We demonstrate the successful application of PINE to a key task in protein NMR spectroscopy: that of converting peak lists extracted from various NMR experiments into assignments associated with probabilities for their correctness. This application, called PINE-NMR, is available from a freely accessible computer server (http://pine.nmrfam.wisc.edu). The PINE-NMR server accepts as input the sequence of the protein plus user-specified combinations of data corresponding to an extensive list of NMR experiments; it provides as output a probabilistic assignment of NMR signals (chemical shifts) to sequence-specific backbone and aliphatic side chain atoms plus a probabilistic determination of the protein secondary structure. PINE-NMR can accommodate prior information about assignments or stable isotope labeling schemes. As part of the analysis, PINE-NMR identifies, verifies, and rectifies problems related to chemical shift referencing or erroneous input data. PINE-NMR achieves robust and consistent results that have been shown to be effective in subsequent steps of NMR structure determination.
Citations by journals
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Proceedings of the National Academy of Sciences of the United States of America
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Proceedings of the National Academy of Sciences of the United States of America
3 publications, 1.75%
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Molecules
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2 publications, 1.17%
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Nature
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Nature
2 publications, 1.17%
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Scientific Reports
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Scientific Reports
2 publications, 1.17%
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Biochemical and Biophysical Research Communications
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Biomolecules
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1 publication, 0.58%
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Journal of Global Optimization
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1 publication, 0.58%
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Analytical and Bioanalytical Chemistry
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Analytical and Bioanalytical Chemistry
1 publication, 0.58%
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Citations by publishers
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10
20
30
40
50
60
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Springer Nature
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Springer Nature
59 publications, 34.5%
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Elsevier
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Elsevier
27 publications, 15.79%
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American Society for Biochemistry and Molecular Biology
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American Society for Biochemistry and Molecular Biology
18 publications, 10.53%
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Oxford University Press
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Oxford University Press
11 publications, 6.43%
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Wiley
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Wiley
11 publications, 6.43%
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Public Library of Science (PLoS)
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Public Library of Science (PLoS)
9 publications, 5.26%
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American Chemical Society (ACS)
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American Chemical Society (ACS)
7 publications, 4.09%
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
4 publications, 2.34%
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Proceedings of the National Academy of Sciences (PNAS)
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Proceedings of the National Academy of Sciences (PNAS)
3 publications, 1.75%
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Portland Press
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Portland Press
1 publication, 0.58%
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Biophysical Society
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Biophysical Society
1 publication, 0.58%
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IEEE
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IEEE
1 publication, 0.58%
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Cambridge University Press
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Cambridge University Press
1 publication, 0.58%
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American Society for Microbiology
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American Society for Microbiology
1 publication, 0.58%
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Hindawi Limited
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Hindawi Limited
1 publication, 0.58%
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American Society of Hematology
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American Society of Hematology
1 publication, 0.58%
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American Association for the Advancement of Science (AAAS)
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American Association for the Advancement of Science (AAAS)
1 publication, 0.58%
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Bahrami A. et al. Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy // PLoS Computational Biology. 2009. Vol. 5. No. 3. p. e1000307.
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Bahrami A., Assadi A. H., Markley J. L., Eghbalnia H. R. Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy // PLoS Computational Biology. 2009. Vol. 5. No. 3. p. e1000307.
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TY - JOUR
DO - 10.1371/journal.pcbi.1000307
UR - https://doi.org/10.1371%2Fjournal.pcbi.1000307
TI - Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy
T2 - PLoS Computational Biology
AU - Bahrami, Arash
AU - Assadi, Amir H.
AU - Markley, John L.
AU - Eghbalnia, Hamid R
PY - 2009
DA - 2009/03/13 00:00:00
PB - Public Library of Science (PLoS)
SP - e1000307
IS - 3
VL - 5
PMID - 19282963
SN - 1553-734X
SN - 1553-7358
ER -
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@article{2009_Bahrami,
author = {Arash Bahrami and Amir H. Assadi and John L. Markley and Hamid R Eghbalnia},
title = {Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy},
journal = {PLoS Computational Biology},
year = {2009},
volume = {5},
publisher = {Public Library of Science (PLoS)},
month = {mar},
url = {https://doi.org/10.1371%2Fjournal.pcbi.1000307},
number = {3},
pages = {e1000307},
doi = {10.1371/journal.pcbi.1000307}
}
Cite this
MLA
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Bahrami, Arash, et al. “Probabilistic Interaction Network of Evidence Algorithm and its Application to Complete Labeling of Peak Lists from Protein NMR Spectroscopy.” PLoS Computational Biology, vol. 5, no. 3, Mar. 2009, p. e1000307. https://doi.org/10.1371%2Fjournal.pcbi.1000307.