Transmembrane Prediction

• DAS (Stockholm University, Sweden)
  Prediction of transmembrane regions in prokaryotes using the Dense Alignment Surface method
  • input format: sequence only
    
  • output: html page with gif image

• HMMTOP (Hungarian Academy of Sciences, Budapest)
  Prediction of transmembrane helices and topology of proteins using Hidden Markov Model
  • input format: fasta, pir/nbrf, swissprot id or accession number
    has options to select
    
  • output: html page

• MEMSAT (UCSF - original version, requires SACS account)
  Prediction Tool using Dynamic Programming
  • input format: sequence or accession/GI number
    
  • output format: html page with TOPO image

• PHD (Columbia University - PredictProtein)
  Advanced page for selecting only transmembrane helices prediction
  • input format: sequence only
    email address required
    select the PHDhtm option from the type of prediction menu
    
  • output: email message

• PRED - TMR (University of Athens, Greece)
  Transmembrane segment prediction in proteins based on a statistical analysis of the SwissProt database

• PSIPRED V2.3 (University College London)
  • input format: sequence only
    enter server, select MEMSAT2 from list of prediction methods
    
  • output format: email message containing prediction

• SOSUI (Tokyo University of Agriculture & Technology)
  Prediction of transmembrane regions using Hydrophobicity Analysis for Topology and Probe Helix Method for Tertial Structure
  Requires JAVA enabled browser
  • input format: sequence only
    
  • output format: html page with hydrophaty plot and helical wheel diagrams of predicted helices

• Split (University of Split, Croatia - Membrane Protein Transmembrane Secondary Structure Prediction Server)
  Prediction Tool using Preference Functions Method

• TMHMM (Center for Biological Sequence Analysis, Technical University of Denmark)
  Prediction of transmembrane helices in proteins using Hidden Markov Model
  • input format: fasta
    
  • output: html page with image of predicted locations

• TMAP (single) (Karolinska Institute, Sweden)
  Prediction Tool using Multiple Alignment
  • input format: sequence only
    
  • output: prediction plus downloadable ps file of the results

• TMAP (multiple) (Karolinska Institute, Sweden)
  Transmembrane detection based on multiple sequence alignment
  • input format: entire gcg msf file
    
  • output: prediction plus downloadable ps file of the results

• TMPred (European Molecular Biology Network, Swiss node)
  Prediction of transmembrane regions and protein orientation
  • input format: sequence, swissprot id or accession number, Genbank gi
    
  • output: html or ascii

• TopPred 2 (Institut Pasteur)
  Topology prediction of membrane proteins using Hydrophobicity Analysis
  • input format: sequence only
    
  • output format: html page (data displayed as graph)

• TSEG (Kyoto University, Japan)
  Prediction Tool using Clustering of reference data and discriminant analysis for Transmembrane SEGment in Proteins

7TM GPCR (Swiss-Model)
Advanced-level search of specialized protein list