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PP Help: Detailed Table Of Contents

1. Introduction
   1. What is PredictProtein (PP)?
   2. How does PP work?
   3. What is META PP?
   4. How to use PP and META-PP?
      1. email
      2. www
   5. What can we do for you?
   6. Responsible administrator
   7. If You Do NOT Receive a reply
2. Quote and copyright
   1. Who are we?
   2. Please cite
   3. Copyright
   4. Protection of data
   5. Feedback
3. Default input and output
   1. Input (WWW)
   2. Input (email)
   3. Default output
   4. Example for input and output
4. Advanced input options
   1. SWISSPROT identifier
   2. FASTA list
   3. PIR list
   4. SAF formatted alignment
   5. MSF formatted alignment
   6. Column formatted prediction
5. Advanced prediction options
   1. PHDsec only
   2. PHDacc only
   3. PHDhtm only
   4. toggle Coils prediction
   5. toggle ProSite reports
   6. toggle SEG reports
   7. toggle ProDom assignment
   8. TOPITS threading
   9. Evaluate prediction accuracy (for developers)
6. Advanced output options
   1. General output
      1. do not mail output
      2. results in HTML
      3. HTML for printouts
      4. HTML + PHD graphics
      5. HTML + PHD graphics for printouts
      6. concise output
   2. Customising alignment
      1. also BLASTP
      2. no alignment
      3. HSSP format
      4. HSSP profiles
      5. report full sequences
   3. Customising PHD
      1. COLUMN format
      2. PHD in MSF
      3. PHD in RDB
      4. PHD in CASP2
      5. format for graph
   4. Customising TOPITS
      1. TOPITS in HSSP
      2. TOPITS in STRIP
      3. TOPITS in special
      4. report full sequences
   5. Toggle defaults
      1. No ProSite
      2. No SEG
      3. No ProDom
      4. No COILS
7. Examples for input formats (required for email submissions)
   1. Single sequence in
   2. FASTA list
   3. PIR list
   4. SAF alignment
   5. MSF alignment
   6. COLUMN (for TOPITS)
   7. COLUMN (for EvalSec)
8. Methods
   • Definition of family
   1. MaxHom : multiple alignment
   2. PSI-BLAST : iterated profile search
   3. ProSite : functional motifs
   4. SEG : composition-bias
   5. ProDom : domain assignment
   6. PredictNLS : nuclear localisation signal
   7. PHDsec : secondary structure
   8. PHDacc : solvent accessibility
   9. Globe : globularity of proteins
   10. PHDhtm : transmembrane helices
   11. PROFsec : secondary structure
   12. PROFacc : solvent accessibility
   13. Coils : coiled-coil regions
   14. CYSPRED : cysteine bridges
   15. Topits : fold recognition by threading
9. Hints
   1. Automatic parsing of PredictProtein output
      
   2. Note
   3. What to expect from predictions?
   4. In a nutshell: how to avoid pitfalls?
   5. Nuts and bolts: what to keep in mind?
      1. Information content in sequence alignment
      2. Cut-off for including homologues in alignment
      3. Quality of multiple sequence alignment
      4. Minimal length of sequences
      5. Insertions in multiple sequence alignment ( avoid this! )
      6. Untypical' proteins
      7. Prediction of transmembrane helices and topology
      8. Reliability indices for PHD predictions
      9. Combining results with that of other methods
      10. Homologue of known structure
      11. Prediction-based threading
   6. Paper describing pitfalls in sequence analysis:
10. News
    1. PP is migrating...
    2. Currently known problems
    3. PP mirrors
    4. PP news 1999
       
    5. PP news 1998
    6. PP news 1997
    7. PP news 1996
11. Additional information
    1. Interested in the PP software?
    2. Links to selected WWW services
    3. Restrictions (watch it!)
    4. Further PP related publications
       1. Structure and structure prediction, in general
       2. WWW services for biologists
       3. Predictions of 1D structure
       4. Prediction-based threading
       5. Alignment
       6. Evaluation and testing
12. If you do NOT receive a reply

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