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This list of protein subcellular localisation prediction tools includes software, databases, and web services that are used for protein subcellular localization prediction. Some tools are included that are commonly used to infer location through predicted structural properties, such as signal peptide or transmembrane helices , and these tools ...
Hirokawa, Boon-Chieng, Mitaku, SOSUI: Classification and secondary structure prediction for membrane proteins, Bioinformatics Vol.14 S.378-379 (1998) ^ Masami Ikeda, Masafumi Arai, Toshio Shimizu, Evaluation of transmembrane topology prediction methods by using an experimentally characterized topology dataset, Genome Informatics 11: 426–427 (2000) ^
A transmembrane domain (TMD) is a membrane-spanning protein domain.TMDs may consist of one or several alpha-helices or a transmembrane beta barrel.Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues.
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure. This list of protein structure prediction software summarizes notable used software tools in protein structure prediction, including homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction.
A transmembrane protein is a type of ... Due to this difficulty and the importance of this class of proteins methods of protein structure prediction based on ...
This causes the cross-prediction between them, which is a weakness of many transmembrane topology predictors. By predicting signal peptides and transmembrane helices simultaneously (Phobius [14]), the errors caused by cross-prediction are reduced and the performance is substantially increased. Another feature used to increase the accuracy of ...
Many prediction methods now exceed the accuracy of some high-throughput laboratory methods for the identification of protein subcellular localization. [ 1 ] [ 2 ] [ 3 ] Particularly, some predictors have been developed [ 4 ] that can be used to deal with proteins that may simultaneously exist, or move between, two or more different subcellular ...
Approaches include homology modeling, protein threading, ab initio methods, secondary structure prediction, and transmembrane helix and signal peptide prediction. In particular, deep learning based on long short-term memory has been used for this purpose since 2007, when it was successfully applied to protein homology detection [ 59 ] and to ...