An HMM posterior decoder for sequence feature prediction that includes homology information

By Lukas Käll, Anders Krogh, Erik L. L. Sonnhammer. Intelligent Systems in Molecular Biology, 2005

343 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0f6d71b9b437b6d536b898d28a444c2587a9267a

How researchers see this paper

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In Molecular Biology

1. David T. Jones
2. Arne Elofsson
3. Christoph Peters
4. Debora Marks
5. Timothy Nugent
6. Andreas Bernsel
7. G. von Heijne
8. Håkan Viklund

Citations in the corpus

• The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015, methodology): “Here,we present an update to the TOPCONS consensus prediction method and its server implementation, including topology prediction methods that can predict signal peptides as well (Philius (15), PolyPhobius (21) and SPOCTO-PUS (22), along with OCTOPUS (20) and SCAMPI (9)).”
• OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar (2008, background): “, 2004), PRO-TMHMM (Viklund & Elofsson, 2004) and PolyPhobius (Käll et al., 2005)), which all detect < 72% of these TM regions.”
• PredictProtein—an open resource for online prediction of protein structural and functional features (2014, neutral): “PolyPhobius (35) and Memsat3 (36)) predicting all membrane helices correctly for about 60% of all proteins.”
• Transmembrane protein topology prediction using support vector machines (2009, methodology): “Phobius [6] uses a HMM to successfully address the problem of signal peptides in TM protein topology prediction, while PolyPhobius [7] further increases accuracy by including homology information.”
• Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors (2015, positive): “Transmembrane topology was predicted using PolyPhobius 49 and validated by consensus prediction using TOPCONS 50 and MEMSAT-SVM 51 .”
• Prediction of membrane-protein topology from first principles (2008, background): “By using the high-resolution benchmark set, SCAMPI and TopPred (cid:1) G were compared against 10 other frequently used topology prediction methods: HMMTOP (4), MEMSAT (26), MEMSAT3 (6), Phobius (17), PolyPhobius (16), PRO-TMHMM (5), PRODIV-TMHMM (5), TMHMM2.”
• Topology Prediction of α-Helical Transmembrane Proteins (2016, background): “Shortly after the first version was released, an extension called PolyPhobius [92] was released.”