Protein Secondary Structure

DSSP

DSSP is a database of secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).

http://swift.cmbi.ru.nl/gv/dssp/

THGS

A web-based database of transmembrane helices in genome sequences.

http://pranag.physics.iisc.ernet.in/thgs/index.html

PDBTM

PDBTM, the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).

http://pdbtm.enzim.hu/

TMPDB

TransMembrane Protein DataBase with Experimentally-Characterized Transmembrane Topologies.

http://bioinfo.si.hirosaki-u.ac.jp/~TMPDB/

OPM

Orientations of Proteins in Membranes (OPM) database. OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.

http://opm.phar.umich.edu/

S S C P

The program SSCP computes predictions for the content of helix, strand, and coil for a given protein using the amino acid composition as the only input information.

http://coot.embl.de/SSCP//

BMC Search Launcher

BCM Search Launcher: Protein Secondary Structure Prediction

http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html

PredictProtein

PredictProtein is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function

http://www.predictprotein.org/

APSSP

Advanced Protein Secondary Structure Prediction Server

http://imtech.res.in/raghava/apssp/

Jpred3

A Secondary Structure Prediction Server

http://www.compbio.dundee.ac.uk/~www-jpred/

PORTER

Protein Secondary Structure Prediction @ University College Dublin

http://distill.ucd.ie/porter/

PSA Server

The Protein Sequence Analysis (PSA) server predicts protein secondary and tertiary structure based on sequence, and is available for researchers who have amino acid sequences for proteins of unknown structure and for which no homologous sequences are known.

http://bmerc-www.bu.edu/psa/request.htm

PSIPRED

The PSIPRED protein structure prediction server allows you to submit a protein sequence, perform a prediction of your choice and receive the results of the prediction via e-mail.

http://bioinf.cs.ucl.ac.uk/psipred/

SOPMA

The Protein Sequence Analysis (PSA) server predicts protein secondary and tertiary structure based on sequence, and is available for researchers who have amino acid sequences for proteins of unknown structure and for which no homologous sequences are known.

http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html

PROF

PROF - Secondary Structure Prediction System

http://www.aber.ac.uk/~phiwww/prof/

Coiled-coil

Prediction of coiled coil regions in proteins.

http://www.russell.embl.de/cgi-bin/coils-svr.pl

Coiled-coil

Prediction of Coiled-Coil Regions in Proteins

http://mendel.imp.ac.at/METHODS/coil.server.html

Paircoil2

Paircoil2 predicts the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm and an updated coiled coil database.

http://groups.csail.mit.edu/cb/paircoil2/

COILS

COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score.

http://www.ch.embnet.org/software/COILS_form.html

Multicoil

MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. If you are only concerned with whether your sequence is or is not a coiled coil, Paircoil2 is likely to be more accurate than Multicoil. To distinguish between dimeric and trimeric coiled coils, continue using Multicoil.

http://groups.csail.mit.edu/cb/multicoil/cgi-bin/multicoil.cgi

2ZIP

Predict Leucine Zippers in your amino acid sequence.

http://2zip.molgen.mpg.de/index.html

AGADIR

algorithm to predict the helical content of peptides.

http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

Helical Wheel Tool

Helical wheel tool for alpha helice prediction.

http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit

Helical Wheel Tool

Helical wheel drawing program by John K. Everett

http://www-nmr.cabm.rutgers.edu/bioinformatics/Proteomic_tools/Helical_wheel/

turnpred

Strand-loop-strand motifs classification into local hairpins and non local diverging turns using nueral networks

http://www.meilerlab.org/web/view.php?section=0&page=6

BETApro

The Server of Predicting Beta-Residue Pair, Strand Pair, Strand Alignment, and Beta-Sheet Architecture

http://www.ics.uci.edu/%7Ebaldig/betasheet.html

BETAPRED2

The aim of BetaTPred2 server is to predict ß turns in proteins from multiple alignment by using neural network from the given amino acid sequence.

http://www.imtech.res.in/raghava/betatpred2/

LOOP-Pred

A template-based loop prediction server.

http://manaslu.aecom.yu.edu/loopred/

Phobius

EBI service to predict transmembrane topology and signal peptides from the amino acid sequence of a protein.

http://www.ebi.ac.uk/Tools/phobius/

Phobius

A combined transmembrane topology and signal peptide predictor

http://phobius.cbr.su.se/

DAS-TMfilter

Transmembrane Prediction server

http://www.enzim.hu/DAS/DAS.html

DAS

The DAS server will predict transmembrane regions of a query sequence.

http://www.sbc.su.se/~miklos/DAS/

TMAP

Transmembrane detection based on multiple sequence alignment

http://bioinfo4.limbo.ifm.liu.se/tmap/index.html

TMAP

Another TMAP serevr

http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py?form=tmap

TMpred

The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins.

http://www.ch.embnet.org/software/TMPRED_form.html

TopPred

TopPred : Topology prediction of membrane proteins

http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py?form=toppred

SPLIT

Server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions.

http://split.pmfst.hr/split/4/

TMMOD

Hidden Markov Models for Transmembrane Protein topology Prediction

http://liao.cis.udel.edu/website/servers/TMMOD/scripts/frame.php?p=submit

PRED-TMR2

PRED-TMR is a method that predicts transmembrane domains in proteins using solely information contained in the sequence itself.

http://athina.biol.uoa.gr/PRED-TMR2/

MINNOU

Membrane protein IdeNtificatioN withOUt explicit use of hydropathy profiles and alignments

http://minnou.cchmc.org/

PRED-TMBB

Prediction of transmembrane beta-strands of the gram-negative bacteria outer membrane proteins.

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

TMDET

TMDET may be used for the detection of the transmembrane regions of membrane proteins using their 3D structure.

http://tmdet.enzim.hu/

BRPROMPT

Bayesian PRediction Of Membrane Protein Topology

http://www.jenner.ac.uk/BPROMPT/

ConPred II

A Consensus Prediction Method for Obtaining Transmembrane Topology Models with High-Reliability

http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/

SVMtm

Transmembrane Domain Predictor

http://ccb.imb.uq.edu.au/svmtm/svmtm_predictor.shtml

TransMem

TransMem is an ANN (Artificial Neural Network) based program for predicting transmembrane domains in proteins.

http://bioinf.uab.es/cgi-bin/trsdb/transmem.cgi

TMBpro

Prediction of transmembrane beta-barrel features and tertiary structure.

http://www.ics.uci.edu/~baldig/tmb.html

TMB-Hunt

Screen sequence sets for potential/candidate transmembrane barrel proteins using whole sequence amino acid composition.

http://www.bioinformatics.leeds.ac.uk/~andy/betaBarrel/AACompPred/aaTMB_Hunt.cgi

TBBpred

Transmembrane Beta Barrel prediction server predicts the transmembrane Beta barrel regions in a given protein sequence. The server uses a forked strategy for predicting residues which are in transmembrane beta barrel regions. Prediction can be done based only on neural networks or based on statistical learning technique - SVM or combination of two methods.

http://www.imtech.res.in/raghava/tbbpred/

PRED-TMBB

Method based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins

http://bioinformatics.biol.uoa.gr/PRED-TMBB/

TMBETA-GENOME

TMBETA-GENOME is a collection of amino acid sequences for all the completed genomes and the annotated trans beta-barrel membrane proteins (TMBs) using different discrimination algorithms.

http://tmbeta-genome.cbrc.jp/annotation/

TMBETA-DISC

Discrimination of Beta-Barrel Membrane Proteins from Amino Acid Sequence.

http://psfs.cbrc.jp/tmbetadisc/

TMBETA-SVM

Discrimination of Outer Membrane Proteins

http://tmbeta-svm.cbrc.jp/

TMBETA-NET

Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins from amino acid sequence.

http://psfs.cbrc.jp/tmbeta-net/

TMBETA-NET

Prediction of Transmembrane Beta Strands in Proteins from amino acid sequence.

http://gibk26.bse.kyutech.ac.jp/~shandar/netasa/tmbeta/index.html

TMHMM

Prediction of transmembrane helices in proteins

http://www.cbs.dtu.dk/services/TMHMM/

DAS-TMfilter

Transmembrane helix prediction with low false-positive rate

http://mendel.imp.ac.at/sat/DAS/DAS.html

HMMTOP

Prediction of transmembrane helices and topology of proteins

http://www.enzim.hu/hmmtop/

TMSTAT

Statistical analysis of amino acid patterns in transmembrane helices

http://bioinfo.mbb.yale.edu/tmstat/

Localizome

The Localizome server predicts TM helix number and TM topology of a eukaryotic protein and presents the result as an intuitive graphic representation. It utilizes hmmpfam to detect the presence of Pfam domains, and a prediction algorithm, Phobius, to predict the TMhelices.

http://localodom.kobic.re.kr/LocaloDom/index.htm

DLP-SVM

Domain linker predictor

http://www.tuat.ac.jp/~domserv/cgi-bin/DLP-SVM.cgi

RONN

Predict protein disorder

http://www.strubi.ox.ac.uk/RONN

IUPred

Prediction of Intrinsically Unstructured Proteins

http://iupred.enzim.hu/IUPred.html

DISOPRED2

Prediction of Protein Disorder Server

http://bioinf.cs.ucl.ac.uk/disopred/disopred.html

Scooby-domain

Scooby-domain (Sequence hydrophobicity predicts domains) is a method to identify globular regions in protein sequence that are suitable for structural studies.

http://zeus.cs.vu.nl/programs/scoobywww/

DisEMBL

Intrinsic Protein Disorder Prediction

http://dis.embl.de/

GlobPlot

Intrinsic Protein Disorder, Domain & Globularity Prediction

http://globplot.embl.de/

DRIPPRED

Web based predictor for disordered regions in proteins

http://www.sbc.su.se/~maccallr/disorder/

DISpro

Protein Disorder Region Prediction

http://www.ics.uci.edu/~baldig/dispro.html

PONDR

Predictor Of Naturally Disordered Regions

http://www.pondr.com/

PreLink

Prediction of unfolded segments in a protein sequence based on amino acid composition.

http://genomics.eu.org/spip/PreLink

SPRITZ

Protein Disorder Prediction

http://protein.cribi.unipd.it/spritz/

DisProt

DisProt Predictor of Intrinsically Disordered Region

http://www.ist.temple.edu/disprot/predictor.php

VSL2

The VSL2 protein disorder predictor exploits the length-depent (heterogenous) amino acid compositions and sequence properties of intrinsically disordered regions to improve the prediction performance.

http://www.ist.temple.edu/disprot/predictorVSL2.php

NORSp

NORSp is a publicly available predictor for disordered regions in protein. Specifically, it predicts long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil.

http://cubic.bioc.columbia.edu/services/NORSp/