Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.

@article{Krogh2001PredictingTP,
  title={Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes.},
  author={Anders Krogh and B. Larsson and Gunnar von Heijne and Erik L. L. Sonnhammer},
  journal={Journal of molecular biology},
  year={2001},
  volume={305 3},
  pages={
          567-80
        }
}
We describe and validate a new membrane protein topology prediction method, TMHMM, based on a hidden Markov model. [...] Key Result We present a detailed analysis of TMHMM's performance, and show that it correctly predicts 97-98 % of the transmembrane helices. Additionally, TMHMM can discriminate between soluble and membrane proteins with both specificity and sensitivity better than 99 %, although the accuracy drops when signal peptides are present.Expand
An improved hidden Markov model for transmembrane protein detection and topology prediction and its applications to complete genomes
TLDR
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TLDR
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TLDR
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TLDR
To improve the accuracy of TMH detection, a machine-learning based predictor is developed, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold.
consensus approach Prediction of partial membrane protein topologies using a data
We have developed a method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods. When evaluated on a test set of experimentally
Prediction of partial membrane protein topologies using a consensus approach
TLDR
A method to reliably identify partial membrane protein topologies using the consensus of five topology prediction methods is developed and it is found that approximately 90% of the partial consensus topologies are correctly predicted in membrane proteins from prokaryotic as well as eukaryotic organisms.
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