The PredictProtein server (Burkhard Rost)
Expert submission form
PHDsec PHDacc PHDhtm TOPITS MaxHom EvalSec Blast ProSite ProDom
PP Help

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If you don't select anything, the default is that all programs are run! ( ? for programs and thresholds)

Type the required information into the fields Description of field (click on description to get help)
Your email address [ watch typpos -:) ]
Password (only for commercial users)
Which type of prediction do you require?
Specify the format for the returned multiple-sequence alignment
Specify the database to be searched for similar proteins
Output options
BLAST Return BLAST output from SWISS-PROT search
PHD msf PHD rdb PHD col PHD casp2 Return additional PHD output
TOPITS hssp TOPITS strip TOPITS own Additional TOPITS output
HTML formatted results HTML for printouts
HTML with PHD graphs HTML with PHD graphs for printouts 		Return result in HTML (for WWW browsers)
Results on FTP site, NOT in email Results not sent to avoid email floods
concise output Fewer explanations of output
do NOT align
do NOT filter returned alignment
do NOT filter alignment used for PHD
 Process alignment
NO prosite NO prodom NO seg NO coils Switch off default methods
(e.g. to reduce output, or to save time)
Expert options: alignment (MaxHom)
USE MaxHom expert options Tick to activate options
IDE = minimal % sequence identity (15 ≤ IDE ≤ 100)
Note: false positives rapidly increase for values < 30%!
Gap open penalty (1 ≤ GO ≤ 50)
Gap extension penalty (1 ≤ GE ≤ 50)
Comparison metric
Maximal hit value (0.5 ≤ SMAX ≤ 50)
Expert options: transmembrane helices (PHDhtm)
USE PHDhtm expert options Tick to activate options
Minimal membrane helix propensity (0 ≤ Phtm ≤ 1)
MIX = 1.0 -> strongest transmembrane helix (HTM) propensity
MIN = 0.5 -> half HTM, half not (will be labelled HTM)
MIN = 0.0 -> anything labelled HTM
Expert options: threading (TOPITS)
USE TOPITS expert options Tick to activate options
Ratio of structure:sequence (0 ≤ MIX ≤ 100)
MIX =100 -> no sequence info;
MIX = 0 -> no structure info (= pairwise alignment)
Number of hits reported (1 ≤ NHITS ≤ 1000)
Gap open penalty (1 ≤ GO ≤ 50)
Gap extension penalty (0.1 ≤ GE ≤ 50)
Comparison metric
Maximal hit value (0.5 ≤ SMAX ≤ 50)
Additional options
(see Easter Eggs)
One-line name of protein (not necessary)
Specify the format of your sequence(s), alignment, or prediction
Either choose a file with the respective information, or ...


Paste, or type your sequence

  • amino acids in one-letter code
  • any number of white spaces allowed
  • non-standard amino acids to 'X'


  • use SRS to get your sequence from a public database

Batch or interactive?
Final action
Wait? How long to wait (status of PP queue)?
Links WWW services for sequence analysis
 Submit to META CUBIC home PROSITE ProDom PredictProtein Mail to PP Help

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