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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).
PDBTM, the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank (PDB).
Orientations of Proteins in Membranes (OPM) database. OPM provides spatial arrangements of membrane proteins with respect to the hydrocarbon core of the lipid bilayer.
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.
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% )
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.
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.
Mobyle, a portal for bioinformatics analyses.
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.
Distill is a suite of public servers for the prediction of structural features of proteins.
SCratch Protein Predictor: Multiple prediciton on protein secondary structure, relative solvent accessibility, relative solvent accessibility, disulphide bridges, disordered regions, and domains.
Secondary Structure Prediction
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.
'Prediction of Secondary Structure by Amino acid Properties' server at the Laboratory of Bioinformatics and Computational Biology of Institute of Food Science, CNR, Italy.
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.
Simultaneous prediction of secondary structure and trans-membrane spans from the protein sequence thus eliminating the necessity to create a consensus prediction from possibly contradicting outputs of several predictors.
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.
This server offers an interactive interface to the secondary structure assignment program STRIDE.
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.
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.
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.
Paircoil2 predicts the parallel coiled coil fold from sequence using pairwise residue probabilitis with the Paircoil algorithm and an updated coiled coil database.
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.
Prediction of Coiled-Coil Regions in Proteins
CCHMMPROF: an hmm-based predictor of coiled-coil segments in proteins.
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.
Helical wheel drawing program by John K. Everett
Helical wheel tool for alpha helice prediction.
Strand, beta-Sheet, beta-turn, Loop & Hairpin Prediction
This service makes a prediction of beta-turns and their type from an amino-acid sequence.
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.
The Server of Predicting Beta-Residue Pair, Strand Pair, Strand Alignment, and Beta-Sheet Architecture
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).
Transmembrane Helix & Topology
EBI service to predict transmembrane topology and signal peptides from the amino acid sequence of a protein.
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.
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.
The DAS server will predict transmembrane regions of a query sequence.
Classification and Secondary Structure Prediction of Membrane Proteins.
Improving the accuracy of predicting transmembrane helices.
Transmembrane helix-helix interaction prediction based on residue contacts.
HMMTOP is an automatic server for predicting transmembrane helices and topology of proteins, developed by G.E. Tusn
Available on the PSIPRED Protein Structure Prediction metaserver.
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.
Membrane protein IdeNtificatioN withOUt explicit use of hydropathy profiles and alignments
Philius Transmembrane Prediction Server.
The purpose of this server is to predict the transmembrane (TM) secondary structures of membrane proteins, using the method of preference functions.
A TMAP server on Mobyle metaserver.
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.
TopPred : Topology prediction of membrane proteins
A transmembrane helical-protein topology predictor.
Transmembrane helix prediction with low false-positive rate
Statistical analysis of amino acid GxxxG patterns in transmembrane helices
PRED-TMR is a method that predicts transmembrane domains in proteins using solely information contained in the sequence itself.
TMDET may be used for the detection of the transmembrane regions of membrane proteins using their 3D structure.
Transmembrane beta-Barrels
Prediction of transmembrane beta-barrel features and tertiary structure.
Discrimination and Prediction of Transmembrane Beta Strands in Outer Membrane Proteins from amino acid sequence.
Method based on a Hidden Markov Model, capable of predicting the transmembrane beta-strands of the gram-negative bacteria outer membrane proteins
BOMP is a tool for prediction of beta-barrel integral outer membrane proteins (BOMPs).
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.
Prediction of membrane spanning segments and topology in beta barrel membrane proteins.
Super-secondary structure prediction of transmembrane ?-barrel proteins.
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.
Discrimination of Beta-Barrel Membrane Proteins from Amino Acid Sequence.
Domain Linkers
Disorder Prediction
DisProt Predictor of Intrinsically Disordered Region
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.
PrDOS is a server to predict natively disordered regions of a protein chain from its amino acid sequence.
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.
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.
metaPrDOS is a meta server to predict natively disordered regions of a protein chain from its amino acid sequence.
Web based predictor for disordered regions in proteins
DPROT is a PSSM based predictor for the prediction of disordered proteins.
iPDA aims to provide an integrated environment for detecting disordered regions and exploring their functional roles.
Sequence-Based Protein Disordered Region Prediction Using Neural Networks.
The Database of Protein Disorder (DisProt) is a curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.
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