DMCA
Predicting Transmembrane Protein Topology with a Hidden Markov Model: Application to Complete Genomes (2001)
Venue: | J. MOL. BIOL |
Citations: | 898 - 17 self |
Citations
5881 | A tutorial on hidden markov models and selected applications in speech recognition
- Rabiner
- 1989
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Citation Context ...is found in a helix, the cytoplasm, or the periplasm is calculated in the following way. The posterior probability of each model state is found by the forward-backward algorithm (Durbin et al., 1998; =-=Rabiner, 1989-=-). These probabilities are then added up for states belonging to each of the three categories. These probabilities are used for plots like Figure 2. The expected number of residues in a transmembrane ... |
788 |
Biological sequence analysis
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- 2004
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Citation Context ...equire that the different segments (helices, inside loops, etc) be cut out of the sequences and the corresponding submodels estimated separately. Instead, we use labeled sequences for the estimation (=-=Durbin et al., 1998-=-; Krogh, 1994, 1997), which is a simple generalization of the standard method that constrains residues labeled as membrane helix to use only states labeled the same, and those labeled as cytoplasmic t... |
786 | Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites.
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Citation Context ...in Data Bank (PDB) and homologous sequences removed as described by Lund et al. (1997). The set is available at the above mentioned web address. A set of signal peptides used for training of SignalP (=-=Nielsen et al., 1997-=-) was used to test the discrimination between signal peptides and membrane helices. This redundancy-reduced set contains 1011 eukaryotic, 141 Gram-positive, and 266 Gram-negative sequences. The sequen... |
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Citation Context ...en subsets with 16 proteins in each. It was made sure that no two proteins from different sets were more than 25 % identical in a Needleman-Wunsch alignment by the ALIGN program in the FASTA package (=-=Pearson, 2000-=-). Within the sets, the similarity was allowed to be higher. Crossvalidation was done by training on all sequences in nine subsets, and testing the accuracy on the subset left out from training. This ... |
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Citation Context ... helices rely on those two signals. Several methods use a sliding window which is predicted as being part of a membrane helix or not, either by a weight matrix (Edelman, 1993) or by a neural network (=-=Rost et al., 1995;-=- Casadio et al., 1996). Some methods use multiple 0022-2836/01/030567±14 $35.00/0 # 2001 Academic Presss568 Predicting Transmembrane Protein Topology alignments to improve on the predictions (Persson... |
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Helix packing in membrane proteins.
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Citation Context ... between ®ve and 25, which translates to helix lengths between 15 and 35 when the caps are included. This is consistent with the distribution of helix lengths in membrane proteins of known structure =-=(Bowie, 1997-=-). In this interval, the length distribution is explicitly represented by the transition probabilities of the transitions in the helix model. The HMM parameters, which are the probabilities of the 20 ... |
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Citation Context ...t between organisms. An interesting new ®nding is that N in-C in topologies are preferred in all organisms except C. elegans. It has previously been noticed that N in topologies are over-represented =-=(Jones, 1998-=-). All N in-C in proteins have an even number of transmembrane helices, and can be thought of as constructed from a succession of ``helical hairpins'', i.e. two transmembrane helices connected by an e... |
44 | A: Hidden Markov models for labeled sequences
- Krogh
(Show Context)
Citation Context ...rent segments (helices, inside loops, etc) be cut out of the sequences and the corresponding submodels estimated separately. Instead, we use labeled sequences for the estimation (Durbin et al., 1998; =-=Krogh, 1994-=-, 1997), which is a simple generalization of the standard method that constrains residues labeled as membrane helix to use only states labeled the same, and those labeled as cytoplasmic to used states... |
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Topological rules for membrane protein assembly in eukaryotic cells
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Citation Context ...d by an extracytoplasmic loop. Experimental studies have suggested that the helical hairpin may act as an independent ``insertion unit'' during membrane protein assembly (Gafvelin & von Heijne, 1994; =-=Gafvelin et al., 1997-=-), and hence that topologies constructed from helical hairpin units may evolve more easily than other topologies. It is also clear from a number of experimental studies that the translocation of N-ter... |
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Quadratic minimization of predictors for protein secondary structure: Application to transmembrane helices
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Citation Context ...methods for prediction of transmembrane helices rely on those two signals. Several methods use a sliding window which is predicted as being part of a membrane helix or not, either by a weight matrix (=-=Edelman, 1993)-=- or by a neural network (Rost et al., 1995; Casadio et al., 1996). Some methods use multiple 0022-2836/01/030567±14 $35.00/0 # 2001 Academic Presss568 Predicting Transmembrane Protein Topology alignm... |
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N-Tail translocation in a eukaryotic polytopic membrane protein: synergy between neighboring transmembrane segments
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Citation Context ...c cells places strong restrictions on thesPredicting Transmembrane Protein Topology 575 Table 5. Statistics on the orientation of predicted membrane proteins Organism amino acid sequence of the tail (=-=Monne et al., 1999-=-; Whitley et al., 1995, 1994), thus working against the appearance of N out topologies during evolution. Multispanning Number of annotated gens Pred TMHs Single spanning C in C out S. cerevisiae 6305 ... |
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2 |
A predictor of transmembrane alpha-helix domains of proteins based on neural networks
- Casadio, Fariselli, et al.
- 1996
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Citation Context ...ose two signals. Several methods use a sliding window which is predicted as being part of a membrane helix or not, either by a weight matrix (Edelman, 1993) or by a neural network (Rost et al., 1995; =-=Casadio et al., 1996)-=-. Some methods use multiple 0022-2836/01/030567±14 $35.00/0 # 2001 Academic Presss568 Predicting Transmembrane Protein Topology alignments to improve on the predictions (Persson & Argos, 1994; Rost e... |
1 | SecAindependent translocation of the periplasmic Nterminal tail of an Escherichia coli inner membrane protein. Position-speci®c effects on translocation of positively charged residues and construction of a protein with a C-terminal translocation signal - Whitley, Gafvelin - 1995 |