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Fast pseudolikeliho...
Fast pseudolikelihood maximization for direct-coupling analysis of protein structure from many homologous amino-acid sequences
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- Ekeberg, Magnus (författare)
- KTH,Beräkningsbiologi, CB
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Hartonen, Tuomo (författare)
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- Aurell, Erik (författare)
- KTH,Beräkningsbiologi, CB,Aalto University, Finland
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(creator_code:org_t)
- Elsevier BV, 2014
- 2014
- Engelska.
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Ingår i: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 276, s. 341-356
- Relaterad länk:
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http://arxiv.org/pdf...
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visa fler...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- Direct-coupling analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. In protein families of realistic size, this learning can only be done approximately, and there is a trade-off between inference precision and computational speed. We here show that an earlier introduced l(2)-regularized pseudolikelihood maximization method called plmDCA can be modified as to be easily parallelizable, as well as inherently faster on a single processor, at negligible difference in accuracy. We test the new incarnation of the method on 143 protein family/structure-pairs from the Protein Families database (PFAM), one of the larger tests of this class of algorithms to date.
Ämnesord
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
Nyckelord
- Contact map
- Direct-coupling analysis
- Inference
- Potts model
- Protein structure prediction
- Pseudolikelihood
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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