Protein Secondary Structure
- Secondary Structure Databases
- Structure Prediction Metaservers
- Secondary Structure Prediction
- Secondary Structure Visualization
- Coiled-Coil Regions
- Leucine Zippers
- Helix
- Strand, beta-Sheet, beta-turn, Loop & Hairpin Prediction
- Transmembrane Helix & Topology
- Transmembrane beta-Barrels
- Domain Linkers
- Disorder Prediction
Secondary Structure Databases
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/
A web-based database of transmembrane helices in genome sequences.
http://pranag.physics.iisc.ernet.in/thgs/index.html
PDBTM, the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).
http://pdbtm.enzim.hu/
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/
Structure Prediction Metaservers
PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions ,structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges.
http://www.predictprotein.org/
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 ?-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS2 is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2=94%), membrane spanning helices (Q2=87%) and secondary structure (Q3 score of 81.3% )
http://wks16338.biology.ualberta.ca/proteus2/
TarO analyses a protein sequence by a large number of bioinformatics techniques. These include crystallisation propensity prediction, orthologue searching, and many other sequence-based calculations.
http://www.compbio.dundee.ac.uk/taro/cgi-taro/targpipe_home.pl?logout=true
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/
Mobyle, a portal for bioinformatics analyses.
http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome
The Bioinformatics Toolkit is a platform that integrates a great variety of tools for protein sequence analysis. Many tools are developed in-house, and serveral public tools are offered with extended functionality. The toolkit includes, among others: NucleotideBLAST, ProteinBLAST, PSI-BLAST, fastHMMER, HHsenser; ClustalW, MUSCLE, Mafft, ProbCons; HHrep, PCOILS, REPPER; Quick2D; HHpred, Modeller; CLANS, ANCESCON, PHYLIP; Reformat, RetrieveSeq, gi2promoter. For a short descrition of the tools, click the section tabs.
http://toolkit.tuebingen.mpg.de/
Distill is a suite of public servers for the prediction of structural features of proteins.
http://distill.ucd.ie/
BCM Search Launcher: Protein Secondary Structure Prediction
http://searchlauncher.bcm.tmc.edu/seq-search/struc-predict.html
SCratch Protein Predictor: Multiple prediciton on protein secondary structure, relative solvent accessibility, relative solvent accessibility, disulphide bridges, disordered regions, and domains.
http://scratch.proteomics.ics.uci.edu/
Using one or more protein sequences as input, it runs different types of analysis and combines their results in the form of a compact, information-rich visualization of protein features. Using this output, it is then possible to perform a detailed visual comparison of structural features that include PFAM domains, propensities for secondary structure elements (helix, strand, loop), propensities for intrinsic disorder (structural flexibility), and predictions of transmembrane regions for a number of proteins.
http://www.proteinarchitect.net/ProteinArchitect/index.jsp
Secondary Structure Prediction
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
Determination the one dimensional secondary structure of proteins (distinguishing ?-helices, ?-strands, and non-regular structures) from primary sequence data which makes use of Parallel Cascade Identification (PCI), a powerful technique from the field of nonlinear system identification.
http://bioinf.sce.carleton.ca/PCISS/start.php
'Prediction of Secondary Structure by Amino acid Properties' server at the Laboratory of Bioinformatics and Computational Biology of Institute of Food Science, CNR, Italy.
http://bioinformatica.isa.cnr.it/PRESSAPRO/
YASPIN is a HNN (Hidden Neural Network) secondary structure prediction program that uses the PSI-BLAST algorithm to produce a PSSM for the input sequence, which it then uses to perform its prediction.
http://www.ibi.vu.nl/programs/yaspinwww/
Prediction of local protein structure from sequence.
http://www2.fz-juelich.de/nic//cbb/service/locustra.php
This server offers an interactive interface to the secondary structure assignment program STRIDE.
http://webclu.bio.wzw.tum.de/cgi-bin/stride/stridecgi.py
Secondary protein structure prediction from sequence using neural networks
http://www.meilerlab.org/view.php?section=0&page=6
A consensus method for protein secondary structure prediction at University of Dundee
http://alexander.compbio.ucsf.edu/~nomi/nnpredict.html
Secondary structure and class prediction server
http://alexander.ucsf.edu/~jmc/pred2ary/index.html
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//
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
Secondary Structure Visualization
Protein structure visualization server can be used to generate schematic representations of secondary structures and relative solvent accessibilities, allowing one to highlight selected residues, e.g. polymorphic or involved in protein-protein interactions.
http://polyview.cchmc.org/
Coiled-Coil Regions
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
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/
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
Prediction of Coiled-Coil Regions in Proteins
http://mendel.imp.ac.at/METHODS/coil.server.html
CCHMMPROF: an hmm-based predictor of coiled-coil segments in proteins.
http://gpcr.biocomp.unibo.it/cgi/predictors/cchmmprof/pred_cchmmprof.cgi
COILED-COIL PREDICTION
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_lupas.html
Leucine Zippers
Helix
HeliQuest calculates from an ?-helix sequence its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.
http://heliquest.ipmc.cnrs.fr/
Helical wheel drawing program by John K. Everett
http://www-nmr.cabm.rutgers.edu/bioinformatics/Proteomic_tools/Helical_wheel/
Helical wheel tool for alpha helice prediction.
http://rzlab.ucr.edu/scripts/wheel/wheel.cgi?sequence=ABCDEFGHIJLKMNOP&submit=Submit
Strand, beta-Sheet, beta-turn, Loop & Hairpin Prediction
This service makes a prediction of beta-turns and their type from an amino-acid sequence.
http://bioserv.rpbs.jussieu.fr/Coudes/COUDES.html
beta-sheet type prediction from sequence.
http://www2.fz-juelich.de/nic//cbb/service/betty.php
The Server of Predicting Beta-Residue Pair, Strand Pair, Strand Alignment, and Beta-Sheet Architecture
http://www.ics.uci.edu/%7Ebaldig/betasheet.html
Prediction of beta-hairpin in protein. Bhairpred server is based on machine learning technique SVM using single sequence information, evolutionary profile, predicted and observed secondary structure (as obtained using Psipred and DSSP), predicted and observed accessibility values (as obtainned from Netasa and DSSP).
http://www.imtech.res.in/raghava/bhairpred/
Transmembrane Helix & Topology
EBI service to predict transmembrane topology and signal peptides from the amino acid sequence of a protein.
http://www.ebi.ac.uk/Tools/phobius/
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
PONGO is an annotation metaserver consisting of six programs for the transmembrane annotation of the human proteome and three methods for the detection of three major post translational modifications, namely the cleavage of signal peptide, the GPI-anchoring, and the disulfide bonding.
http://pongo.biocomp.unibo.it/
The DAS server will predict transmembrane regions of a query sequence.
http://www.sbc.su.se/~miklos/DAS/
Classification and Secondary Structure Prediction of Membrane Proteins.
http://bp.nuap.nagoya-u.ac.jp/sosui/
Improving the accuracy of predicting transmembrane helices.
http://www.csbio.sjtu.edu.cn/bioinf/MemBrain/
Transmembrane helix-helix interaction prediction based on residue contacts.
http://bio-cluster.iis.sinica.edu.tw/~bioapp/TMhit/
HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins, developed by G.E. Tusn
http://www.enzim.hu/hmmtop/html/submit.html
Available on the PSIPRED Protein Structure Prediction metaserver.
http://bioinf.cs.ucl.ac.uk/psipred/
MetaTM is a consensus method for predicting transmembrane (TM) topologies. It is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors.
http://metatm.sbc.su.se/
Membrane protein IdeNtificatioN withOUt explicit use of hydropathy profiles and alignments
http://minnou.cchmc.org/
Philius Transmembrane Prediction Server.
http://www.yeastrc.org/philius/pages/philius/runPhilius.jsp;jsessionid=EF8989D84441C40AE2E0DC97B3E9A2A6
The purpose of this server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions.
http://split.pmfst.hr/split/4/
A TMAP server on Mobyle metaserver.
http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py?form=tmap
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 : Topology prediction of membrane proteins
http://mobyle.pasteur.fr/cgi-bin/MobylePortal/portal.py?form=toppred
A transmembrane helical-protein topology predictor.
http://sparks.informatics.iupui.edu/Softwares-Services_files/tups.htm
Transmembrane helix prediction with low false-positive rate
http://mendel.imp.ac.at/sat/DAS/DAS.html
Statistical analysis of amino acid GxxxG patterns in transmembrane helices
http://bioinfo.mbb.yale.edu/tmstat/
Hidden Markov Models for Transmembrane Protein topology Prediction
http://liao.cis.udel.edu/website/servers/TMMOD/scripts/frame.php?p=submit
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/
TMDET may be used for the detection of the transmembrane regions of membrane proteins using their 3D structure.
http://tmdet.enzim.hu/
A Consensus Prediction Method for Obtaining Transmembrane Topology Models with High-Reliability
http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/
TransMem is an ANN (Artificial Neural Network) based program for predicting transmembrane domains in proteins.
http://bioinf.uab.es/cgi-bin/trsdb/transmem.cgi
Transmembrane beta-Barrels
Prediction of transmembrane beta-barrel features and tertiary structure.
http://www.ics.uci.edu/~baldig/tmb.html
Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins from amino acid sequence.
http://psfs.cbrc.jp/tmbeta-net/
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/
BOMP is a tool for prediction of beta-barrel integral outer membrane proteins (BOMPs).
http://services.cbu.uib.no/tools/bomp
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
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/
Prediction of membrane spanning segments and topology in beta barrel membrane proteins.
http://rbf.bioinfo.tw/~sachen/BARRELpredict/TMBETAPRED-RBF.php
Super-secondary structure prediction of transmembrane ?-barrel proteins.
http://bioinformatics.bc.edu/clotelab/transFold/
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/
Discrimination of Beta-Barrel Membrane Proteins from Amino Acid Sequence.
http://psfs.cbrc.jp/tmbetadisc/
Domain Linkers
Disorder Prediction
DisProt Predictor of Intrinsically Disordered Region
http://www.ist.temple.edu/disprot/predictor.php
FoldIndex tries to answer to the question: Will this protein fold? It's a dynamic and interactive process that estimates the local and general probability for the provided sequence, under specified conditions, to fold.
http://bip.weizmann.ac.il/fldbin/findex
PrDOS is a server to predict natively disordered regions of a protein chain from its amino acid sequence.
http://prdos.hgc.jp/cgi-bin/top.cgi
POODLE (Prediction Of Order and Disorder by machine LEarning) is a system that predicts disorder regions using amino acid sequence alone. The POODLE system consists of three predictions, short disorder regions prediction, long disorder regions prediction and unfolded protein prediction.
http://mbs.cbrc.jp/poodle/index.html
MeDor (Metaserver of Disorder) helps to identify protein disorder by providing a graphical interface with a unified view of the output of multiple disorder predictors. It allows fast, simultaneous analysis of a query sequence by multiple predictors and easy comparison of the prediction results.
http://www.vazymolo.org/MeDor/index.html
metaPrDOS is a meta server to predict natively disordered regions of a protein chain from its amino acid sequence.
http://prdos.hgc.jp/cgi-bin/meta/top.cgi
Web based predictor for disordered regions in proteins
http://www.sbc.su.se/~maccallr/disorder/
DPROT is a PSSM based predictor for the prediction of disordered proteins.
http://www.imtech.res.in/raghava/dprot/home.html
iPDA aims to provide an integrated environment for detecting disordered regions and exploring their functional roles.
http://biominer.bime.ntu.edu.tw/ipda/
Sequence-Based Protein Disordered Region Prediction Using Neural Networks.
http://casp.rnet.missouri.edu/predisorder.html
TOP Intrinsically Disordered Protein Scale Prediction
http://www.disprot.org/dev/disindex.php
