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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 ...
Simple Modular Architecture Research Tool (SMART) is a biological database that is used in the identification and analysis of protein domains within protein sequences. [ 1 ] [ 2 ] SMART uses profile-hidden Markov models built from multiple sequence alignments to detect protein domains in protein sequences.
Method description Type Link Initial release RaptorX-SS8 predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles: Webserver/downloadable: server download: 2011 GOR: Information theory/Bayesian inference: Many implementations: Basic GOR GOR V: 2002 (GOR V) Jpred
In this case, more sensitive methods are required to identify more remotely related proteins or protein families. From these relationships, hypotheses about the protein's functions, structure, and domain composition can be inferred. HHsearch performs searches with a protein sequence through databases.
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.
PredictProtein (PP) is an automatic service that searches up-to-date public sequence databases, creates alignments, and predicts aspects of protein structure and function. Users send a protein sequence and receive a single file with results from database comparisons and prediction methods.
Method that uses the distribution of hydrophobic and electrostatic patches on the surface of the protein, factoring in the intensity and relative orientation of the respective surface patches into an aggregation propensity function that has been trained on a benchmark set of 31 adnectin proteins. sequence - Amyloidogenic regions AggreRATE-Pred [48]
However, RaptorX is also significantly different from profile-based methods (e.g., HHPred and Phyre2) in that RaptorX excels at modeling of protein sequences without a large number of sequence homologs by exploiting structure information. RaptorX Server has been designed to ensure a user-friendly interface for users inexpert in protein ...
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