2-D Structure Prediction
This is collection of freely accessible web tools for the prediction of various structural features of proteins based on the protein sequence.
| open in new windowBioinformatics Toolkit | This toolkit is a collection of a wide range of tools and links for sequence analysis, function, and structure prediction. This resource offers convenient web interfaces for many freely available tools. |
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| open in new windowDistill | A suite of public servers for the prediction of structural features of proteins by recursive neural networks and remote homology information. The predictions include secondary structure, backbone structural motifs, relative solvent accessibility, coarse contact maps and coarse protein structures. |
| open in new windowGeneSilico | This is a gateway to various methods for protein structure prediction. Including domains identification, secondary structure, transmembrane and disorder prediction. |
| open in new windowMobyle | Platform that integrates variety of tools for protein sequence and structure analysis and prediction. Mobyle includes tools for secondary structure prediction , disorder prediction , membrane proteins topology and more. |
| open in new windowPredictProtein | Platform that integrates variety of tools for protein sequence analysis and the prediction of protein structure and function. |
| open in new windowProteinArchitect | Integration of several algorithms for domains, disorder, transmembrane prediction and multiple sequence alignment. The server focused on visual approach for protein comparison of different protein features above the sequence level. |
| open in new windowProteinCCD | Crystallographic Construct Design. ProteinCCD functions as a meta-server, concerning secondary structure, disorder, coiled coils, transmembrane segments, domains and domain linkers. The required input is the DNA and not the protein sequence, as such the software can automatically design the oligonucleotides needed for PCR amplification of the constructs. |
| open in new windowPROTEUS | Platform that integrates several algorithms for signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction and homology modeling. |
| open in new windowSCRATCH | Platform that integrates variety of tools for protein sequence analysis and the prediction of protein structure. The predictions include solvent accessibility, secondary structure, contact map, domain, disorder and disulfide bonds |
| open in new windowTarO | TarO offers a single point of reference for key bioinformatics analyses relevant to selecting proteins or domains for study by structural biology techniques, including crystallisation propensity, disorder, domains and phosphorylation sites predictions |
| open in new windowTRAMPLE | Platform that integrates several algorithms for secondary structure, transmembrane helices, strands, and signal peptides prediction. |
| open in new windowConserved Domains | Domain search by sequence homology |
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| DOMAC | Hybrid approach uses the template-based method to predict domains for proteins having homologous template structures and the ab initio method based on DOMpro for de novo proteins |
| open in new windowDomPred | Fold-recognition based method for domain prediction |
| open in new windowDOMpro | Domains prediction using neural networks from MSAs and predicted secondary structure information |
| open in new windowGlobPlot | Domain prediction by delineating predicted disordered, non-globularregions from the globular ones based on amino acid preferences |
| open in new windowInterProScan | Domain search by sequence homology |
| Meta-DP | Consensus prediction based on several predictors (DOMpro, InterProScan, GlobPlot and more) |
| open in new windowPURE | Multi-step protocol for prediction of unassigned regions |
| Shandy | Ab initio and homology based prediction of protein domains by recursive neural networks |
| open in new windowCDM | |
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| open in new windowJPRED | Consensus prediction based on various methods |
| open in new windowPCI-SS | |
| Porter (Distill) | |
| open in new windowPraline | Multiple sequence alignment program that include secondary structure prediction |
| open in new windowpredator (Mobyle) | |
| open in new windowPreSSAPro | |
| PROFsec | |
| open in new windowPSA | |
| open in new windowPSIPRED | |
| open in new windowSSpro (SCRATCH) | |
| open in new windowCCHMMPROF | |
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| open in new windowCOILS | |
| open in new windowCOILS | |
| open in new windowMulticoil | Distinguish between dimeric and trimeric coiled coils |
| open in new windowPaircoil2 | |
| open in new windowBETTY | β-Sheet type (antiparallel and parallel strands) prediction |
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| open in new windowBhairPred | Prediction of β-hairpins in proteins. |
| open in new windowCOUDES | prediction of beta-turns and their type |
| open in new windowLOCUSTRA | |
| Porter+ (Distill) | |
| open in new windowPREDICT-2ND |
| open in new windowDiANNA | |
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| DISULFIND | |
| open in new windowDIpro (SCRATCH) | |
| GDAP | |
| open in new windowMetalDetector | |
| PreCys | |
| open in new windowCMAPpro (SCRATCH) | |
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| NNcon | |
| SPINE-2D | |
| SVMcon | |
| XXStout (Distill) | |
| open in new windowMetalDetector | |
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(Helical transmembrane proteins found in all membranes except in the outer membrane of Gram-negative bacteria) |
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| ConPred | Consensus topology prediction based on various methods. Includes signal peptides prediction. |
| open in new windowDAS-TMfilter | Prediction of putative transmembrane helices |
| open in new windowHMMTOP | Topology prediction |
| Localizome | Topology prediction |
| open in new windowMemBrain | Topology prediction. Includes signal peptides prediction. Improved helix ends predidction |
| open in new windowMEMSAT3 | Topology prediction |
| open in new windowMEMSAT-SVM | Topology prediction. Includes signal peptides and re-entrant helix prediction. |
| open in new windowMetaTM | Consensus topology prediction |
| open in new windowMINNOU | Prediction of putative transmembrane helices |
| orienTM | Topology prediction |
| open in new windowPHDhtm | Topology prediction |
| open in new windowPhobius | Combined topology and signal peptide prediction. |
| open in new windowPhilius | Combined topology and signal peptide prediction. |
| PONGO | Topology prediction. Includes signal peptides prediction |
| open in new windowSOSUI | Prediction of putative transmembrane helices |
| open in new windowSPLIT4 | Prediction of putative transmembrane helices |
| open in new windowSVMtm | Prediction of putative transmembrane helices |
| TMhit | Transmembrane helix-helix interaction prediction based on residue contacts |
| open in new windowTMHMM | Topology prediction |
| open in new windowTMpred | Topology prediction |
| open in new windowTOPCONS | Consensus topology prediction |
| TopPred | Topology prediction |
| TUPS | Topology prediction. Includes signal peptides prediction |
β-Barrel Integral Membrane Proteins |
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(β-Barrel transmembrane proteins found in the outer membrane of Gram-negative bacteria, mitochondria and chloroplasts) |
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| open in new windowBOMP | Prediction of putative transmembrane barrels. |
| open in new windowHHomp | Prediction of putative transmembrane barrels. |
| open in new windowPRED-TMBB | Topology prediction. |
| PROFtmb | Topology prediction. |
| TMB-Hunt | Prediction of putative transmembrane barrels |
| TMBETA-NET | Prediction of putative transmembrane barrels |
| open in new windowTMBETAPRED-RBF | Topology prediction. |
| open in new windowTMBpro | Topology and 3-D structure prediction |
| open in new windowtransFold | Topology prediction |
Signal Peptides |
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Most prediction methods are prone to predict N-terminal signal peptides as transmembrane helix. Some of the above predictors include signal peptide prediction. Here is a list of independent N-terminal signal peptide predictors. |
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| open in new windowPRED-SIGNAL | prediction of signal peptides in archaea |
| open in new windowRED-LIPO | Prediction of lipoprotein and secretory signal peptides in Gram-positive bacteria |
| open in new windowLipoP | Prediction of lipoproteins and signal peptides in Gram negative bacteria |
| open in new windowSignalP | |
| open in new windowSignal-3L | |
| open in new windowSIG-Pred | |
| open in new windowSOSUIsignal | |