List of protein secondary structure prediction programs

List of protein secondary structure prediction programs

Name Method descriptionTypeLinkInitial release
SPIDER2 The most comprehensive and accurate prediction by iterative Deep Neural Network (DNN) for protein structural properties including secondary structure, local backbone angles, and accessible surface area (ASA)Webserver/downloadableserver/download2015
s2D Predicts disorder and secondary structure in one unified framework. Trained on solution-based NMR data.Webserver/downloadableserver/download2015
RaptorX-SS8 predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profilesWebserver/downloadableserver download2011
NetSurfP Profile-based neural networkWebserver/downloadableserver2009
GOR Information theory/Bayesian inferenceMany implementationsBasic GOR GOR V2002 (GOR V)
Jpred Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts secondary structure and solvent accessibilityWebserverserver and API1998
Meta-PP Consensus prediction of other serversWebserverserver1999
PREDATOR Knowledge-based database comparisonWebserverserver1997
PredictProtein Profile-based neural networkWebserverserver1992
PSIPRED two feed-forward neural networks which perform an analysis on output obtained from PSI-BLASTWebserverserver1999
SOPMA Self OPtimised Prediction Method from multiple Alignments (based on nearest neighbour method)Webserverserver1995
Homology Modeling Professional for HyperChem Frequency analysis of amino acid residues observed in proteinsCommercialalgorithm2002
SymPred an improved dictionary based approach which captures local sequence similarities in a group of proteinsWebserverserver2004
YASSPP Cascaded SVM-based predictor using PSI-BLAST profilesWebserverserver2006
PSSpred Multiple backpropagation neural network predictors from PSI-BLAST profilesWebserver/downloadable programserver and downloadable program2012
HCAM Hidropathy Clustering Assisted Method by detection of physicochemical patternsdownloadable program plus databasemain page2013
Frag1D Prediction of both secondary structure and Shape Strings (discrete states of dihedral angles) using profile based fragment matchingWebserver/downloadable programmain page2010

See also

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