PROTEIN SECONDARY STRUCTURE

Precautionary Quote: "We should be quite remiss not to emphasize that despite the
popularity of secondary structural prediction schemes, and the almost ritual
performance of these calculations, the information available from this is of limited
reliability. This is true even of the best methods now known, and much more so of the
less successful methods commonly available in sequence analysis packages. Running
a secondary structure prediction on a newly-determined sequence just because
everyone else does so, is to be deplored, and the fact that the results of such
predictions are generally ignored is insufficient justification for doing and publishing
them." Arthur Lesk, 1988. See here for a more recent evaluation (Reference: Yang
Y et al. (2018) Brief Bioinformatics 19(3): 482–494).

JPred4 - is the latest version of the popular JPred protein secondary

structure prediction server which provides predictions by the JNet
algorithm, one of the most accurate methods for secondary structure
prediction. In addition to protein secondary structure, JPred also makes
predictions of solvent accessibility and coiled-coil regions.
(Reference: Drozdetskiy A et al. (2015) Nucleic Acids
Res 43(W1): W389–W394).

RaptorX - RaptorX excels at secondary, tertiary and contact prediction

for protein sequences without close homologs in the Protein Data Bank
(PDB). RaptorX predicts protein secondary and tertiary structures,
contact and distance map, solvent accessibility, disordered regions,
functional annotation and binding sites. RaptorX also assigns confidence
scores to predicted structures.(Reference: Yang Y et al. (2018) Brief
Bioinformatics 19(3): 482–494).

PredictProtein 2013 (Technical University of Berlin, Germany) - they have

substantially expanded the breadth of structural annotations, e.g. by adding
predictions of non-regular secondary structure and intrinsically disordered regions,
disulphide bridges and inter-residue contacts, and finally by also covering trans-
membrane beta barrels structures. They have also added important resources for
the prediction of protein function. registration required.

PEP2D (G.P.S. Raghava, Scientist & Head Bioinformatics Center, Institute of

Microbial Technology, India) - this Peptide Secondary Structure Prediction
server that allows users to predict regular secondary structure in their
peptides (e.g., H: Helix, E:Strand, C:Coil). Till date all the secondary
structure prediction methods are optimized for proteins. Peptides may
adopt diffrent secondary structure when integrated in proteins. Thus it is
important to develop seperate method for predicting secondary structure
 of peptides instead of using protein secondary structure prediction
methods.

2dSS (Biologie Computationnelle et Quantitative, Sorbonne Université,

Paris, France) - is a web-server for visualising and comparing secondary
structure predictions. It provides two main functionalities: 2D-alignment
and compare predictions. The view 2D-alignment has been designed to
visualise conserved secondary structure elements in a multiple sequence
alignment (MSA). From this one can study the secondary structure
content of homologous proteins (a protein family) and highlight its
structural patterns.

PROTEUS2 - is a web server designed to support comprehensive protein

structure prediction and structure-based annotation. PROTEUS2 accepts either
single sequences (for directed studies) or multiple sequences (for whole proteome
annotation) and predicts the secondary and, if possible, tertiary structure of the
query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal
peptide identification, transmembrane helix prediction, transmembrane β-strand
prediction, secondary structure prediction (for soluble proteins) and homology
modeling (i.e. 3D structure generation) into a single prediction pipeline.
(Reference: Montgomerie S et al. (2008) Nucleic Acids Res. 36(Web Server
issue): W202-209).

mCSM-membrane - predicts the effects of mutations on

transmembrane proteins. (Reference: Pires DEV et al. 2020. Nucl Acids
Res 48 (W1): W147–W153).

For a metasite linked to a wide range of protein sequence analysis and structure
predictions online programs, I recommend PredictProtein (ROSTLAB,
Technische Universität München). Also see: SCRATCH Protein
Predictor (Institute for Genomics & Bioinformatics, University of California, Irvine,
U.S.A.)

Several great sites for online analysis of potential membrane spanning proteins
are: (Test sequence ; see Orientation of Proteins in Membranes for 268 unique a-
helical membrane protein structures)

TMpred - Prediction of trans-membrane regions and orientation

- ISREC (Swiss Institute for Experimental Cancer Research)
TMHMM - Prediction of transmembrane helices in proteins (Center for
Biological Sequence Analysis, The Technical University of Denmark)
DAS - Transmembrane Prediction Server (Stockholm University, Sweden)
SPLIT (D. Juretic, Univ. Split , Croatia) - the transmembrane protein topology
prediction server provides clear and colourful output including beta preference and
modified hydrophobic moment index.
OCTOPUS - Using a novel combination of hidden Markov models and artificial neural
networks, OCTOPUS predicts the correct topology for 94% of the a dataset of 124
sequences with known structures. (Reference: Viklund, H. & Elofsson, A. 2008.
Bioinformatics 24: 1662-1668)

Phobius - is a combined transmembrane topology and signal peptide predictor

(Reference: L. Käll et al. 2004. J. Mol. Biol. 338: 1027-1036) This tool can also be
accessed here (EBI).

CCTOP (Consensus Constrained TOPology prediction) server - utilizes 10

different state-of-the-art topology prediction methods, the CCTOP server
incorporates topology information from existing experimental and
computational sources available in the PDBTM, TOPDB and TOPDOM
databases using the probabilistic framework of hidden Markov model. The
server provides the option to precede the topology prediction with signal
peptide prediction and transmembrane-globular protein discrimination.
(Reference: Dobson L et al. (2015) Nucleic Acids Res 43(W1): W408–W412).
 TMFoldWeb - is the web server implementation of TMFoldRec, a
transmembrane protein fold recognition algorithm. TMFoldRec uses statistical
potentials and utilizes topology filtering and a gapless threading algorithm. It
ranks template structures and selects the most likely candidates and
estimates the reliability of the obtained lowest energy model. The statistical
potential was developed in a maximum likelihood framework on a
representative set of the PDBTM database. According to the benchmark test
the performance of TMFoldRec is about 77 % in correctly predicting fold class
for a given transmembrane protein sequence. (Reference: Kozma D &
Tusnády GE (2015) Biol Direct. 10: 54).

MEMSATSVM - is an improved transmembrane protein topology prediction

using SVMs. This method is capable of differentiating signal peptides from
transmembrane helices. (Reference: Reeb J et al.
(2015) Proteins; 83(3): 473-84).
 MEMEMBED - prediction of membrane protein orientation. is able to
quickly and accurately orientate both alpha-helical and beta-barrel membrane
proteins within the lipid bilayer, showing closer agreement with experimentally
determined values than existing approaches. We also demonstrate both
consistent and significant refinement of membrane protein models and the
effective discrimination between native and decoy structures
(Reference: Nugent T & DT Jones (2013) BMC Bioinformatics 14: 276)

RHYTHM - predicts the orientation of transmembrane helices in channels and

membrane-coils, specifically buried versus exposed residues. (Reference: A. Rose et al.
2009. Nucl. Acids Res. 37(Web Server issue):W575-W580)

TMMOD - Hidden Markov Model for Transmembrane Protein Topology

Prediction (Dept. Computer & Information Sciences, University of Delaware,
U.S.A.) - on the results page click on "show posterior probabilities" to see a TMHMM-
type diagram

PRED-TMR2 (C. Pasquier & [Link],Dept. Cell Biology and Biophysics,

Univ. Athens, Greece) - when applied to several test sets of transmembrane proteins
the system gives a perfect prediction rating of 100% by classifying all the sequences in
the transmembrane class. Only 2.5% error rate with nontransmembrane proteins.

TOPCONS - computes consensus predictions of membrane protein topology using

a Hidden Markov Model (HMM) and input from five state-of-the-art topology prediction
methods. (Reference: A. Bernsel et al. 2009. Nucleic Acids Res. 37(Webserver issue),
W465-8) . For a batch server without BLAST runs use TOPCONSsingle.

MINNOU (Membrane protein IdeNtificatioN withOUt explicit use of hydropathy profiles

and alignments) - predicts alpha-helical as well as beta-sheet transmembrane (TM)
domains based on a compact representation of an amino acid residue and its
environment, which consists of predicted solvent accessibility and secondary structure
of each amino acid. (Reference: Cao et al. 2006. Bioinformatics 22: 303-309). A legend
to help interpret the results in here.
 SuperLooper - provides the first online interface for the automatic, quick and
interactive search and placement of loops in proteins. (Reference: P.W. Hildebrand et al.
2009. Nucl. Acids Res. 37(Web Server issue):W571-W574) )

Transmembrane Kink Predictor (TMKink) - A hallmark of membrane protein structure

is the large number of distorted transmembrane helices. Because of the prevalence of
bends, it is important to not only understand how they are generated but also to learn
how to predict their occurrence. Here, we find that there are local sequence preferences
in kinked helices, most notably a higher abundance of proline, which can be exploited to
identify bends from local sequence information. A neural network predictor identifies
over two-thirds of all bends (sensitivity 0.70) with high reliability (specificity 0.89).
(Reference: Meruelo AD et al. 2011. Protein Sci. 20:1256-64)

SCMMTP Scoring Card Method Membrane Transport Proteins : Identifying and

characterizing membrane transport proteins using propensity scores of dipeptides. The
training and test accuracies of SCMMTP are 83.81% and 76.11%, respectively.
(Reference: Vasylenko, T. et al. 2015. BMC Bioinformatics, 16 (Suppl 1):S8, 2015)

For drawing the structure of transmembrane proteins two sites are available:

Protter - an open-source tool for interactive integration and visualization of annotated

and predicted protein sequence features together with experimental proteomic
evidence. Protter supports numerous proteomic file formats and automatically integrates
a variety of reference protein annotation sources, which can be readily extended via
modular plug-ins. A built-in export function produces publication-quality customized
protein illustrations, also for large datasets. (Reference: U. Omasits et al. 2014.
Bioinformatics. 30:884-886). Diagram of the holin from bacteriophage lambda
generated with Protter:

TOPO2 (S. Johns, UCSF Sequence Analysis Consulting Service, U.S.A.) - this site
provides considerable control over the presentation. Extensive documentation is
provided here.

TMRPres2D (TransMembrane protein Re-Presentation in 2 Dimensions tool) - this

Java tool takes data from a variety of protein folding servers and creates uniform, two-
dimensional, high analysis graphical images/ models of alpha-helical or beta-barrel
transmembrane proteins. (Reference: I.C. Spyropoulos et al. 2004.
Bioinformatics 20: 3258-3260).

Signal peptide recognition & subcellular localization:

A. Bacterial proteins

PSORTb (Brinkman Lab, Simon Fraser Univ., Canada) - provides probably the most
accurate bacterial protein subcellular localization predictor. Alternatively
use PSORT (Univ. Tokyo, Japan) - a series of programs for the prediction of protein
localization sites in cells. Choose programs specific for for animal, yeast, plant or
bacterial ( Gram-negative or Gram- positive) proteins.
PSLpred - is a SVM based method, predicts 5 major subcellular localization
(cytoplasm, inner-membrane, outer- membrane, extracellular, periplasm) of Gram-
negative bacteria. This method includes various SVM modules based on different
features of the proteins. The hybrid approach achieved an overall accuracy of 91%,
which is best among all the existing methods for the subcellular localization of
prokaryotic proteins. (Reference: M. Bhasin et al. (2005) Bioinformatics 21: 2522-2524.)

CELLO subCELlular LOcalization predictive system - assigns Gram-negative

proteins to the cytoplasm , inner membrane, periplasm, outer membrane or extracellular
space with overall prediction accuracy of ca. 89% . Also analyzes eukaryotic and Gram-
positive proteins. (Reference: C.S. Yu et al. 2004. Protein Sci. 13:1402-1406). The
updated CELLO2GO (Protein subCELlular LOcalization Prediction with
Functional Gene Ontology Annotation) - CELLO2GO should be a useful tool for
research involvingcomplex subcellular systems because it combines CELLO and
BLAST into one platform and its output is easily manipulated such that the user-specific
questions may be readily addressed (Reference: Yu CS et al. 2014. PLoS
ONE 9: e99368).

SignalP - predicts the presence and location of signal peptide cleavage sites in Gram-
positive, Gram-negative and eukaryotic proteins (Center for Biological Sequence
Analysis, The Technical University of Denmark). For an example of a periplasmic
protein use test sequence MalE.
Phobius - is a combined transmembrane topology and signal peptide predictor
(Reference: L. Käll et al. 2004. J. Mol. Biol. 338: 1027-1036).
LipoP 1.0 (Center for Biological Sequence Analysis Technical University of
Denmark) - allows prediction of where signal peptidases I & II cleavage sites from Gram
negative bacteria will cleave a protein.

SecretomeP - produces ab initio predictions of non-classical i.e. not signal peptide

triggered protein secretion. The method queries a large number of other feature
prediction servers to obtain information on various post-translational and localizational
aspects of the protein, which are integrated into the final secretion prediction
(Reference: J.D. Bendtsen et al. 2005. BMC Microbiology 5: 58).

SSPRED - Identification & classification of proteins involved in bacterial secretion

systems. Do not submit more than four proteins at once. (Reference: Pundhir, S., &
Kumar, A. 2011. Bioinformation 6: 380-382).

Signal Find Server - includes (a) FlaFind which predicts archaeal class III
(type IV pilin-like) signal peptides (class III signal peptides) and their prepilin
peptidase cleavage sites; (b) EppA-pilinFind which predicts class III signal
peptides processed by a unique archaeal prepilin peptidase, EppA; (c)
TatFind which predicts archaeal AND bacterial Twin-Arginine Translocation
(Tat) signal peptides; (d) PilFind which predicts bacterial type IV pilin-like
signal peptides and their prepilin peptidase cleavage sites; and, (e) TatLipo
which predictes haloarchaeal Tat signal peptides that contain a SPase II
cleavage site (lipobox).

Signal-3L 2.0 - is an online server for predicting the N-terminal protein signal
peptide, and the input is the amino acid sequence only. It is constructed with a
hierarchical mixture model, which contains the following three layers: (1)
Discrimination of SP (Signal Peptide) proteins and TMH (TransMembrane
Helical) proteins from the other globular proteins; (2) Recognizing SP proteins
from TMH proteins; and, (3) Identifying the cleavage sites of SP proteins.
(Reference: Y-Z. Zhang & H-B. Shen. Journal of Chemical Information and
Modeling, 2017, 57: 988-999)

PrediSi - PREDIction of SIgnal peptides (Karsten Hiller, Technical University

of Braunschweig)

Signal Find Server - provides several distinct programs: (a) FlaFind predicts
archaeal class III (type IV pilin-like) signal peptides (class III signal peptides)
and their prepilin peptidase cleavage sites. (b) EppA-pilinFind predicts class III
signal peptides processed by a unique archaeal prepilin peptidase, EppA. (c)
TatFind predicts archaeal AND bacterial Twin-Arginine Translocation (Tat)
signal peptides. (d) PilFind predicts bacterial type IV pilin-like signal peptides
and their prepilin peptidase cleavage sites. (e) TatLipo predictes haloarchaeal
Tat signal peptides that contain a SPase II cleavage site (lipobox).

B. Eukaryotic proteins

DeepLoc-1.0 predicts the subcellular localization of eukaryotic proteins. It

can differentiate between 10 different localizations: Nucleus, Cytoplasm,
Extracellular, Mitochondrion, Cell membrane, Endoplasmic reticulum,
Chloroplast, Golgi apparatus, Lysosome/Vacuole and Peroxisome. Their
model achieves a good accuracy (78% for 10 categories; 92% for membrane-
bound or soluble), outperforming current state-of-the-art algorithms, including
those relying on homology information. (Reference: Almagro Armenteros JJ et
al. 2017. Bioinnformatics; 33(21): 3387-3395).

Protein Prowler Subcellular Localisation Predictor version 1.2 accepts

amino acid sequences, presented in the FASTA format, and determines the
localisation of the protein among the following categories: Secretory pathway
(presence of a signal peptide SP); Mitochondrion (presence of a
mitochondrial targeting peptide mTP); Chloroplast (presence of a chloroplast
transit peptide cTP; only applicable to plant proteins); and, Other (nucleus,
cytoplasmic, or otherwise). (Reference: Bodén, M. and Hawkins
(2005) Bioinformatics. 21(10): 2279-2286).
WoLF PSORT - (National Institute of Advanced Science and Technology,
Japan) (Reference: Horton P et al. (2007) Nucleic Acids Res. 35(Web Server
issue): W585–W587).

ngLOC - is an n-gram-based Bayesian classifier that predicts subcellular

localization of proteins both in prokaryotes and eukaryotes. The overall
prediction accuracy varies from 85.3% to 91.4% across species. This program
can predict 11 distinct locations each in plant and animal species. ngLOC also
predicts 4 and 5 distinct locations on gram-positive and gram-negative
bacterial datasets, respectively. (Reference: King BR et al. 2012. BMC Res
Notes. 5: 351).

ProtComp (Softberry, U.S.A.) can be used to predict the subcellular localization for
animal/fungal and plant proteins.

SecretomeP - produces ab initio predictions of non-classical i.e. not signal peptide

triggered protein secretion. The method queries a large number of other feature
prediction servers to obtain information on various post-translational and localizational
aspects of the protein, which are integrated into the final secretion prediction
(Reference: J.D. Bendtsen et al. 2005. BMC Microbiology 5: 58).

Other sites for secondary structure predictions include:

JPred4 - is the latest version of the popular JPred protein secondary structure
prediction server which provides predictions by the JNet algorithm, one of the most
accurate methods for secondary structure prediction. In addition to protein secondary
structure, JPred also makes predictions of solvent accessibility and coiled-coil regions.
JPred4 features higher accuracy, with a blind three-state (a-helix, ß-strand and coil)
secondary structure prediction accuracy of 82.0% while solvent accessibility prediction
accuracy has been raised to 90% for residues <5% accessible. (Reference: A.
Drozdetskiy et al. [Link]. Acids Res. 43 (W1): W389-W394).

Network Protein Sequence @nalysis at IBCP - (Institut de Biologie et Chemie des

Proteines, Lyon, France) - has DSC, GORIV, Predator, SOPMA and Heirarchical
Neural Network Method plus older programs.

PSIPRED Protein Sequence Analysis Workbench - includes PSIPRED v3.3 (Predict

Secondary Structure); DISOPRED3 & DISOPRED2 (Disorder Prediction);
pGenTHREADER (Profile Based Fold Recognition); MEMSAT3 & MEMSAT-SVM
(Membrane Helix Prediction); BioSerf v2.0 (Automated Homology Modelling); DomPred
(Protein Domain Prediction); FFPred 3 (Eukaryotic Function Prediction);
GenTHREADER (Rapid Fold Recognition); MEMPACK (SVM Prediction of TM
Topology and Helix Packing) pDomTHREADER (Fold Domain Recognition); and,
DomSerf v2.0 (Automated Domain Modelling by Homology). (Reference: Buchan DWA
et al. 2013. Nucl. Acids Res. 41 (W1): W340-W348).

For a full range of properties of your protein including hydrophobicity, alpha helix,
beta-sheet plots see ProScale (ExPASy, Switzerland).

Disordered states:

Many proteins containing regions that do not form well-defined structures and the
following new programs help define these regions:

D2P2 (Database of Disordered Protein Predictions) - A battery of disorder

predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and
IUPred, were run on all vast number of protein sequences. Searches are
provided against the database; and links are provided to each of the
disordered servers. (Reference: Oates ME et al. (2013). Nucleic Acids
Res 41(D1): D508-D516).
 RONN (Regional Order Neural Network) - (Reference: Z.R. Yang et al. 2005.
Bioinformatics 21: 3369-3376). For explanation of native disorder see here.
IUPred - The underlying assumption is that globular proteins are composed of amino
acids which have the potential to form a large number of favorable interactions, whereas
intrinsically unstructured proteins (IUPs) adopt no stable structure because their amino
acid composition does not allow sufficient favorable interactions to form.
(Reference: Z. Dosztányi et al. 2005. Bioinformatics 21: 3433-3434).
DISOPRED3 (Reference: J.J. Ward et al. 2004. J. Molec. Biol. 337: 635-645).

PrDOS is a server to predict natively disordered regions of a protein chain

from its amino acid sequence. PrDOS returns disorder probability of each
residue as prediction results.(Reference: Ishida T, & Kinoshita K (2007)
Nucleic Acids Res. 35(Web Server issue): W460-4.).

MFDp (Multilayered Fusion-based Disorder predictor) - aims to improve over the

current disorder predictors.(Reference: M.J. Mizianty et al. 2010.
Bioinformatics 26: i489-i496)

MoRFpred - Molecular recognition features (MoRFs) are short binding regions

located within longer intrinsically disordered regions that bind to protein partners via
disorder-to-order transitions. MoRFs are implicated in important processes including
signaling and regulation. MoRFpred is a computational tool for sequence-based
prediction and characterization of short disorder-to-order transitioning binding regions in
proteins which identifies all MoRF types (a, ß, coil and complex). (Reference: F.M.
Disfani et al. 2012. Bioinformatics 28: i75-i83).

Scooby-domain (Sequence hydrophobicity predicts domains) is a method to identify

globular regions in protein sequence that are suitable for structural studies. The
Scooby-domain JAVA applet can be used as a tool to visually identify 'foldable' regions
in protein sequence. Interesting graphics. (Reference: R.A. George et al. 2005. Nucl.
Acids Res. 33: W160-W163).

For estimations on the antigenicity of regions of proteins see:

Antigenicity Plot (JaMBW module) - Given a sequence of amino acids, this program
computes and plots the antigenicity along the polypeptide chain, as predicted by the
algorithm of Hopp & Woods (1981).
SAbPred - is a structure-based antibody prediction server (Reference: J.
Dunbar et al. Nucleic Acids Res. 2016; 44(Web Server issue): W474–W478.

EMBOSS Antigenic (EMBOSS package) - this program predicts potentially antigenic

regions of a protein sequence, using the method of Kolaskar & Tongaonkar (1990). Also
accessible here.
 OptimumAntigen™ Design Tool (GenScript) - peptides are optimized using
the industry's most advanced antigen design algorithm. Each peptide is
measured against several protein databases to confirm the desired epitope
specificity. Benefits of using the OptimumAntigen™ Design Tool include
avoidance of unexposed epitopes, ability to specify desired cross-reactivity,
strong antigenicity of chosen peptide, identification of the best conjugation and
presentation options for your desired assay(s), use of built in peptide tutorial
for synthesis and solubility, and guaranteed immune response.

EpiC (The ProteomeBinders Epitope Choice Resource) collates and

presents a structure-function summary and antigenicity prediction of your
protein to help you design antibodies that are appropriate to your planned
experiments. (Reference: Haslam, N. & Gibson. T. Proteome Res., 2010, 9
(7): 3759–3763).

SVMTriP - is a method to predict antigenic epitopes using support vector

machine to integrate tri-peptide similarity and propensity. (Reference: B. Yao
et al. PLoS ONE (2012); 7(9):e45152).

To screen for coiled-coil regions in proteins use:

Coils - prediction of coiled coil regions in troteins (Swiss node of EMBnet,

Switzerland) - (Reference: A. Lupas et al. 1991 Science 252: 1162-1164). See
also PCOILS and MARCOILS.
Paircoils (MIT Laboratory for Computer Science, U.S.A.) - (Reference: B. Berger et
al. 1995. Proc. Natl. Acad. Sci. USA, 92: 8259-8263) or MultiCoil - is based on the
PairCoil algorithm and is used for locating dimeric and trimeric coiled coils.
(Reference: E. Wolf et al. 1997. Protein Sci. 6: 1179-1189). CoilP

REPPER (REPeats and their PERiodicities) - detects and analyzes regions with short
gapless repeats in proteins. It finds periodicities by Fourier Transform (FTwin) and
internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids
that reflect certain properties, for instance hydrophobicity, and gives information on
corresponding periodicities. REPwin uses self-alignments and displays repeats that
reveal significant internal similarities. They are complemented by PSIPRED and coiled
coil prediction (COILS), making the server a useful analytical tool for fibrous proteins.
(Reference: M. Gruber et al. 2005. Nucl. Acids Res. 33: W239-W243).

Beta-barrel outer membrane proteins: (Test sequence)

PRED-TMßß (Bagos, P. G., et al. Dept Cell Biology & Biophysics, University of
Athens, Greece) - employs a Hidden Markov Model method, capable of predicting and
discriminating beta-barrel outer membrane proteins. Gives one the opportunity to
download a custom image plot or a 2D representation (see below):
 BetaTPred2 (Bioinformatics Center, Institute of Microbial Technology, India) - predict
ß turns in proteins from multiple alignment by using neural network from the given
amino acid sequence. For ß turn prediction, it uses the position specific score matrices
generated by PSI-BLAST and secondary structure predicted by PSIPRED. For a
classification of the ß turn type use BetaTurns.

BOMP - The ß-barrel outer membrane protein predictor (Reference: Berven, F.S. et
al. 2004. Nucl. Acids Res. 32 (Web Server issue):W394-9 ).

HHomp - detection of outer membrane proteins by HMM-HMM comparisons

ConBBPred - Consensus Prediction of Transmembrane Beta-Barrel Proteins - gives

one a choice of eight prediction programs.

Metasite:

Scratch Protein Predictor - (Institute for Genomics and Bioinformatics, University

California, Irvine) - programs include: ACCpro: the relative solvent accessibility of
protein residues; CMAPpro: Prediction of amino acid contact maps; COBEpro:
Prediction of continuous B-cell epitopes; CONpro: predicts whether the number of
contacts of each residue in a protein is above or below the average for that residue;
DIpro: Prediction of disulphide bridges; DISpro: Prediction of disordered regions;
DOMpro: Prediction of domains; SSpro: Prediction of protein secondary structure;
SVMcon: Prediction of amino acid contact maps using Support Vector Machines; and,
3Dpro: Prediction of protein tertiary structure (Ab Initio).

MESSA: Meta-Server for protein sequence analysis - provides secondary

structure (PSIPRED, SSPRO); coil and loop (DISEMBL) and flexible loop
(DISEMBL) analysis, identification of low complexity (SEG) and disordered
regions (IsUnstruct, DISOPRED, DISEMBL,DISPRO); transmembrane helices
(TMHMM, TOPPRED,HMMTOP, MEMSAT); TM Helices and signal peptides
(MEMSAT_SVM, Phobius); signal peptides (SignalP HMM Mode, SignalP NN
Mode); coiled coils (COILS) and positional conservation. Multiple Sequence
Alignment of confident BLAST hits, filtered by less than 90% identity and more
than 40% coverage, are used to calculate the positional conservation indices
of residues in the sequence. The conserved residues usually play important
roles in maintaining the function or structure of a protein. The residues are
highlighted from white, through yellow to dark red as the conservation level
increases. Function Prediction: This section contains predicted function
annotation, GO terms and EC numbers (if the query is an enzyme). A
confidence level ("very confident", "confident" or "probable") is provided for
each prediction. (Reference: Q. Cong & N.V. Grishin. BMC Biology
2012, 10:82).

Quick2D - overview of secondary structure including coiled-cois, transmembrane

helices and disordered regions.