List of protein secondary structure

prediction programs
List of protein secondary structure prediction programs
 Initial
Name Method description Type Link
release
Porter 5 (https://d Fast, state-of-the-art ab initio server/download
oi.org/10.1101/28 prediction of protein secondary Webserver/downloadable (http://distilldee 2018
9033) structure in 3 and 8 classes p.ucd.ie/porter/)
The most comprehensive and
accurate prediction by iterative Deep
server/download
Neural Network (DNN) for protein
(http://sparks-la
SPIDER2 structural properties including Webserver/downloadable 2015
b.org/server/SPI
secondary structure, local backbone
DER2/)
angles, and accessible surface area
(ASA)
server/download
Predicts disorder and secondary (http://www-mvs
s2D structure in one unified framework. Webserver/downloadable oftware.ch.cam. 2015
Trained on solution-based NMR data. ac.uk/index.php/
s2D)
server (http://rap
torx.uchicago.ed
predict both 3-state and 8-state
u) download (htt
RaptorX-SS8 secondary structure using conditional Webserver/downloadable 2011
p://ttic.uchicago.
neural fields from PSI-BLAST profiles
edu/~jinbo/softw
are.htm)
server (http://ww
NetSurfP Profile-based neural network Webserver/downloadable w.cbs.dtu.dk/ser 2009
vices/NetSurfP/)
Basic GOR (htt
p://abs.cit.nih.go
v/gor/) GOR V 2002
GOR Information theory/Bayesian inference Many implementations (https://archive.i (GOR
s/20141016030 V)
756/http://gor.b
b.iastate.edu/)
Multiple Neural network assignment server and API
from PSI-BLAST and HMMER profiles. (http://www.com
Jpred Webserver 1998
Predicts secondary structure and pbio.dundee.ac.
solvent accessibility uk/jpred)
server (http://ww
w.cs.bgu.ac.il/~
Meta-PP Consensus prediction of other servers Webserver dfischer/predictp 1999
rotein/submit_m
eta.html)
server (https://w
eb.archive.org/w
eb/2007102422
Knowledge-based database 5855/http://biow
PREDATOR Webserver 1997
comparison eb.pasteur.fr/se
qanal/interfaces/
predator-simple.
html)
server (http://ww
PredictProtein Profile-based neural network Webserver w.predictprotein. 1992
org/)
two feed-forward neural networks server (http://bio
PSIPRED which perform an analysis on output Webserver inf.cs.ucl.ac.uk/ 1999
obtained from PSI-BLAST psipred/)
 SOPMA Self OPtimised Prediction Method Webserver server (https://n 1995
from multiple Alignments (based on psa-prabi.ibcp.f
nearest neighbour method) r/NPSA/npsa_s
opma.html)
Homology
Modeling
algorithm (http://
Professional for
Frequency analysis of amino acid www.molfunctio
HyperChem (htt Commercial 2002
residues observed in proteins n.com/bioinform
p://www.molfuncti
atics.htm)
on.com/software1.
htm)
server (https://w
eb.archive.org/w
an improved dictionary based
eb/2014102721
approach which captures local
SymPred Webserver 0156/http://bio-c 2004
sequence similarities in a group of
luster.iis.sinica.e
proteins
du.tw/SymPre
d/)
server (https://ar
chive.is/201212
Cascaded SVM-based predictor using
YASSPP Webserver 12204452/http:// 2006
PSI-BLAST profiles
yasspp.cs.umn.
edu/)
server and
downloadable
Multiple backpropagation neural
Webserver/downloadable program (http://z
PSSpred network predictors from PSI-BLAST 2012
program hanglab.ccmb.m
profiles
ed.umich.edu/P
SSpred/)
Hidropathy Clustering Assisted
downloadable program main page (htt
HCAM Method by detection of 2013
plus database p://acbrc.org/)
physicochemical patterns
Prediction of both secondary structure
main page (htt
and Shape Strings (discrete states of Webserver/downloadable
Frag1D p://frag1d.biosh 2010
dihedral angles) using profile based program
u.se)
fragment matching

See also
List of protein structure prediction software
Protein structure prediction

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