Prediction of membrane-protein topology from first principles

By Andreas Bernsel, Håkan Viklund, J. Falk, Erik Lindahl, G. von Heijne, Arne Elofsson. Proceedings of the National Academy of Sciences of the United States of America, 2008

318 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/31843de4a865fe6d5d6761b9593eab09b5de3431

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Citations in the corpus

TOPCONS: consensus prediction of membrane protein topology (2009, methodology): “Due to the computational limitations arising from the need to run BLAST (18) (Figure 1), only one sequence per query is allowed using TOPCONS, and the prediction typically takes 10–30 s. For large benchmark sets and full proteome scans, the SCAMPI server, implementing only the single-sequence versio”
A decade and a half of protein intrinsic disorder: Biology still waits for physics (2013, background): “Also, the distinctive environment of the membrane bilayer imposes constraints on the amino acid composition of integral membrane proteins, even on the regions external to the membrane bilayer.(116,117)”
Accurate de novo structure prediction of large transmembrane protein domains using fragment-assembly and correlated mutation analysis (2012, unknown): “8105Z : [4]”
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).”
Prediction of the human membrane proteome (2010, methodology): “…human membrane proteome, the a -helical human membrane proteins were predicted from the 47237 gene products of the 21 416 annotated genes in the human genome [28] using seven selected methods: MEMSAT3 [18], MEMSAT-SVM [14], Phobius [16], SCAMPI [19], SPOCTOPUS [17], TMHMM [15], and THUMBUP [27].”
Topology Prediction of α-Helical Transmembrane Proteins (2016, background): “SCAMPI [96] is based on the idea to take biological knowledge and translate it into a computational model.”