List of protein secondary structure prediction programs

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List of protein secondary structure prediction programs

Name Method description Type Link Initial release
Porter 5 Fast, state-of-the-art ab initio prediction of protein secondary structure in 3 and 8 classes Webserver/downloadable server/download 2018
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/downloadable server/download 2015
s2D Predicts disorder and secondary structure in one unified framework. Trained on solution-based NMR data. Webserver/downloadable server/download 2015
RaptorX-SS8 predict both 3-state and 8-state secondary structure using conditional neural fields from PSI-BLAST profiles Webserver/downloadable server download 2011
NetSurfP Profile-based neural network Webserver/downloadable server 2009
GOR Information theory/Bayesian inference Many implementations Basic GOR GOR V 2002 (GOR V)
Jpred Multiple Neural network assignment from PSI-BLAST and HMMER profiles. Predicts secondary structure and solvent accessibility Webserver server and API 1998
Meta-PP Consensus prediction of other servers Webserver server 1999
PREDATOR Knowledge-based database comparison Webserver server 1997
PredictProtein Profile-based neural network Webserver server 1992
PSIPRED two feed-forward neural networks which perform an analysis on output obtained from PSI-BLAST Webserver server 1999
SOPMA Self OPtimised Prediction Method from multiple Alignments (based on nearest neighbour method) Webserver server 1995
Homology Modeling Professional for HyperChem Frequency analysis of amino acid residues observed in proteins Commercial algorithm 2002
SymPred an improved dictionary based approach which captures local sequence similarities in a group of proteins Webserver server 2004
YASSPP Cascaded SVM-based predictor using PSI-BLAST profiles Webserver server 2006
PSSpred Multiple backpropagation neural network predictors from PSI-BLAST profiles Webserver/downloadable program server and downloadable program 2012
HCAM Hidropathy Clustering Assisted Method by detection of physicochemical patterns downloadable program plus database main page 2013
Frag1D Prediction of both secondary structure and Shape Strings (discrete states of dihedral angles) using profile based fragment matching Webserver/downloadable program main page 2010

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