OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar
By Håkan Viklund, Arne Elofsson. 2008
395 citations recorded by the source corpus.
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Christoph Peters
- István Reményi
- László Dobson
- Gábor E. Tusnády
- Arne Elofsson
- Andreas Bernsel
- Lukas Käll
- Nanjiang Shu
Citations in the corpus
- Improving homology modeling from low-sequence identity templates in Rosetta: A case study in GPCRs (2020, methodology): “Membrane spanning topology files were generated by submitting the sequence of the target proteins to Octopus [31].”
- Prediction of the human membrane proteome (2010, methodology): “For improved accuracy, some methods also use sequence similarity searches to incorporate evolutionary information [14, 17–20].”
- 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)).”
- CCTOP: a Consensus Constrained TOPology prediction web server (2015, methodology): “Ten methods were selected based on their availability and performance on different benchmark sets: HMMTOP (28,40), MemBrain (41), MEMSAT-SVM (42), Octopus (43), Philius (44), Phobius (37), Pro-and Prodiv-TMHMM (45), Scampi-MSA (38) and TMHMM (2,39).”
- TOPCONS: consensus prediction of membrane protein topology (2009, methodology): “We also present an implementation of TOPCONS as a web-server based on the individual topology prediction methods OCTOPUS (9), PRO-TMHMM and PRODIVTMHMM (10), SCAMPI-single and SCAMPI-multi (11).”
- Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP (2016, background): “Topology predictors [15], [16] classify residues as inside/outside the cell or organelle and in the membrane (for definitions for the OPM (Orientations of Proteins in Membranes) database [11], see http://opm.”