Improving the accuracy of transmembrane protein topology prediction using evolutionary information
By David T. Jones. Bioinform., 2007
460 citations recorded by the source corpus.
Subfields: Biophysics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/859d219f97d64a093fc0f12e8b4bad91b96d7d0a
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In Biophysics
- Erik Lindahl
- Lorenza Bordoli
- Torsten Schwede
- Christoph Peters
- J. Falk
- Lukas Käll
- Arne Elofsson
- Andreas Bernsel
In Molecular Biology
- Arne Elofsson
- Torsten Schwede
- Christoph Peters
- Lorenza Bordoli
- Yang Zhang
- Liam J. McGuffin
- Björn Wallner
- Andreas Bernsel
Citations in the corpus
- The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides (2015, methodology): “Along these lines, several algorithms for the prediction of (cid:2) -helical TM protein topology exist, either as single-sequence-based methods (8–16) or with the inclusion of homologous sequences in the prediction process (17–22).”
- Prediction of membrane-protein topology from first principles (2008, methodology): “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.”
- Prediction of the human membrane proteome (2010, methodology): “Many of the latest topology prediction methods are based on machine learning techniques, where the predictor is trained on a set of membrane proteins with known topology and ‘‘learns’’ to predict the topology of other proteins based on patterns extracted from the training set [14–18].”
- Topology Prediction of α-Helical Transmembrane Proteins (2016, methodology): “The 3rd version of MEMSAT was presented in 2007 by Jones [94].”
- Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal (2012, methodology): “Protein sequence structure and function annotation programs: InterProScan (60) for protein domain motifs and families recognition, PsiPred (61) for secondary structure prediction, DisoPred (62) for disorder prediction and MEMSAT (63) to predict transmembrane segments.”
- The Phyre2 web portal for protein modelling, prediction and analysis (2015, background): “Identical residues in the alignment are highlighted with a gray background. phyre Investigator (optional) 35| The Phyre Investigator interface is composed of several sections ( Fig.”
- TOPCONS: consensus prediction of membrane protein topology (2009, methodology): “Using a dataset of 163 sequences with known topology, the performance of TOPCONS was benchmarked against eight other topology prediction algorithms (Table 1). ConPredII (7) is an earlier consensus transmembrane topology prediction approach, and the other methods [OCTOPUS (9), MEMSAT3 ( 13 ), SCAMPI ”