Transmembrane domains
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TmPRED
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. The prediction is made using a combination of several weight-matrices for scoring
DAS-domain prediction
Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method (Stockholm University).
Topology
TopPred 2 Pscan. DAS. TopPred 2. Servers. Department. Molscript. Stockholm University Protein Prediction Servers STOCKHOLM UNIVERSITY Theoretical Chemistry Protein Prediction Servers. TopPred 2. Topology prediction of membrane proteins ...
PredTMR
PRED-TMR is a method that predicts transmembrane domains in proteins using solely information contained in the sequence itself.
HMMTOP
Prediction of transmembrane helices and topology of proteins. Prediction of transmembrane helices and topology of proteins
TMAP
Identification of transmembrane segments on a protein sequence alignment or single sequence.
BPROMPT
A consensus server for membrane protein prediction. BRPROMPT (Bayesian PRediction Of Membrane Protein Topology), uses a Bayesian Belief Network to combine the results of other prediction methods, providing a more accurate consensus prediction. Topology predictions with accuracies of 70% for prokaryotes and 53% for eukaryotes were achieved.
SOSUI
Classification and Secondary Structure Prediction of Membrane Proteins, Mitaku Group, Department of Biotechnology, Tokyo University of Agriculture and Technology
TMH Benchmark
Static benchmarking of membrane helix predictions - automatic web server evaluating new methods of transmembrane helices prediction. Features of benchmarking include (i) any new method is compared to the battery of well-established tools; (ii) the battery of measures explored allows spotting strengths in methods that may not be ‘best’ overall. In particular, we report per-residue and per-segment scores for accuracy and the error-rates for confusing membrane helices with globular proteins or signal peptides. An additional feature is that developers can directly investigate any hydrophobicity scale for its potential in predicting membrane helices.
DAS-TMfilter
Predicts transmembrane segments by Dense Alignment Surface method (updated and modified version of the original DAS).
TMBETA-NET
Prediction of Transmembrane Beta Strands in Proteins from amino acid sequence.
TBBPred
Transmembrane Beta Barrel prediction server. 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.
ConPred II
ConPred II. Consensus Prediction Method for Obtaining Transmembrane Topology Models with High-Reliability
http://psfs.cbrc.jp/tmbeta-net
To predict transmembrane strands, enter your sequence in a single letter code in the following box.. Sample sequence: MAPKDNTWYTGAKLGWSQYHDTGLINNNGPTHENKLGAGAFGGYQVNPYVGFEMGYDWLG RMPYKGSVENGAYKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADTYSNVYGKNHDTGV ...
PRED-TMR: Prediction of Transmembrane regions in proteins
Version 1.0 A novel method for predicting transmembrane segment in proteins based on a statistical analysis of the SwissProt database Pasquier, C., Promponas, V.J., Palaios, G.A., Hamodrakas, J.S. and Hamodrakas, S.J. Department of Cell ...
Phobius
Phobius. A combined transmembrane topology and signal peptide predictor Normal prediction. Constrained prediction. PolyPhobius. Instructions. Download. Normal prediction. Paste your protein sequence here in Fasta format: Or: Select the ...
MINNOU protein trans-membrane domain prediction server
MINNOU Membrane protein IdeNtificatioN withOUt explicit use of hydropathy profiles and alignments. Query options E-Mail address Sequence name Amino acid sequence (one letter code) Make relative lipid accessibility prediction using model ...
TMDET: Detection of transmembrane regions
Detection of transmembrane regions by using 3D structure of proteins Version 1.0 Sun 26 Nov, 2006 General info. Form. Manual. Faq. Articles. PDBTM. Comment. TMDET home page TMDET may be used for the detection of the transmembrane regions ...
http://www.bioinformatics.leeds.ac.uk/betaBarrel
TMB-Hunt TransMembrane Barrel-Hunt.
TMHMM Server, v. 2.0
CBS. CBS Prediction Servers. TMHMM TMHMM Server v. 2.0. Prediction of transmembrane helices in proteins Update Nov. 29 2001: Minor change to the html output. NOTE: You can submit many proteins at once in one fasta file. Please limit each ...
TMAP
TMAP. : Displays membrane spanning regions (EMBOSS). your e-mail ( = conditionally required) Input section. Output section. Input section. your e-mail Some explanations about the options. Input section. .sequences - gapprotein ...
http://www.psipred.net
There is nothing here. Please click. To be redirected.
The kPROT server
The kPROT server: A sequence-derived scale for membrane protein structure prediction The Bioinformatics and Biological Computing Unit. and Genome Center. at the Weizmann Institute of Science. , Rehovot, Israel and Department of ...
PRED-TMBB: Prediction of TransMembrane Beta-Barrel Proteins
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. Bagos, P. G., Liakopoulos, Th. D. Spyropoulos I. C., and S. J. Hamodrakas. Department of Cell Biology and Biophysics, Faculty of ...
TMSTAT: Statistical analysis of transmembrane sequences
Statistical analysis of amino acid patterns in transmembrane domains. Includes for download a homology purged database of putative transmembrane domains from SwissProt v.37.
SOSUI WWW Server
Classification and Secondary Structure Prediction of Membrane Proteins. Mitaku Group Department of Biotechnology Tokyo University of Agriculture and Technology mailto: sosui@proteome.bio.tuat.ac.jp. [Naogoya. / TUAT. ]. SOSUI system. ...
TopPred
TopPred. : Topology prediction of membrane proteins (Heijne, Wallin, Claros, Deveaud, Schuerer. ). your e-mail ( = conditionally required) your e-mail Some explanations about the options. Main parameters. enter either the name of a file or ...
TSEG HomePage
TSEG Prediction Tool for Transmembrane SEGment in Proteins. What is TSEG ?. (Manual) Tool for Detecting Membrane Proteins in Genome Sequence. Executing TSEG. Links to Other Prediciton Tools for Transmembrane Proteins. ( In Daisuke Kihara's ...
ProperTM web service
roperTM calculates properties associated with positions in a sequence alignment. The methods employed in this program are designed to analyze membrane proteins and G-protein coupled receptors (GPCRs), but some of the options (i.e the calculation of a cons
Sequence Comparison using Bipartite Scheme with SWAT
Sequence Comparison using Bipartite Scheme with SWAT Sequence Comparison for Transmembrane Sequences. The user specifies the regions he considers to be transmembrane in the sequence, and then chooses the substitution scoring matrices to be ...
http://www.enzim.hu/hmmtop/submit.html
Warning!. Sorry, the HMMTOP homepage had been rearranged. The submission form can be found here.
SVMtm Predictor Teasdale Group IMB
SVMtm is a support vector machine based transmembrane helices predictor. The SVMtm Predictor has been tested to work with multiple protein sequences uploaded in plain text FASTA fromat.
Localizome
A knowledge-based transmembrane topology predictor. 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 ...
