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PP Help 11: Additional information

ADDITIONAL INFORMATION

Interested in the PP software?

• PredictProtein is not easily portable, yet. To make it become a program that can easily by ported to any location (running UNIX or LINUX platforms) is on my list of things-to-do.
• PHD codes are available, respectively will be in the near future (mail to rost@columbia.edu).
• All WWW pages are public. That is: no restrictions to downloading them (provided you keep the reference!).
  download all files from the PP home directory! (How to use your local version?)

Links to selected WWW services

1. General sites 1:
   search engines, literature, pathways, genomes
2. General sites 2:
   literature, pathways, genomes
3. Databases
   general, miscellaneous, DNA/RNA, protein sequences, protein structures
4. Services
   hotlists, general, data base searches, analysing DNA/RNA, protein structure prediction
5. Software
   general, documentation, alignments, homology modelling, threading

Restrictions (watch it!)

• If there are only a few homologous protein sequences in the database that are not too similar to the one you sent (pairwise sequence identity > 90%), prediction accuracy drops for structure predictions (secondary structure, accessibility, transmembrane helices).
• In the multiple sequence alignment returned to you, only homologues down to 30% identity over 80 or more residues are included. This cutoff is five percentage points above the threshold for structural homology (Sander & Schneider, 1991), in an attempt to stay clearly off the twilight zone of sequence similarity, and provide high-quality multiple alignments in an automated fashion.
• The alignment procedure MaxHom is optimised on globular water-soluble proteins. For transmembrane proteins, the alignments of the more hydrophobic transmembrane segments may require changes in the alignments. Furthermore, in particular for transmembrane regions, often more distantly related sequences could be aligned by hand based on hydrophobicity analyses. Unfortunately, we cannot provide such refinements of the alignment automatically.
• If you don't (explicitly request a prediction of transmembrane helices, possible HTM's may not be detected as a particular threshold is applied to avoid over-prediction.
• Functional sequence motifs from ProSite are reported only if found.
• Coiled-coil regions are predicted only if the signal for these detected by the COILS program exceeds a minimal threshold (of 0.5).

Further PP related publications

• Structure and structure prediction, in general
  1. B Rost: Marrying structure and genomics, Structure, 1998, 6, 259-263. (full paper on WWW)
  2. M Andrade, SI O'Donoghue & B Rost: Adaptation of protein surfaces to subcellular location, J. Mol. Biol., 1998, 276, 517-525. (full paper on WWW)
  3. B Rost: Protein structure prediction in 1D, 2D, and 3D, in: P von Ragué Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman and HFI Schaefer (eds.), Encyclopedia of computational chemistry, Sussex: John Wiley & Sons, 1998, in press (1997).. (full paper on WWW)
  4. B Rost and C Sander: 3rd Generation Prediction Of Secondary, in: D. W. Webster (ed.) Predicting protein structure'. Humana Press, 1998, in press. (full paper on WWW)
  5. B Rost: Protein structures sustain evolutionary drift, Folding & Design, 1997, 2, 519-524 (1997).. (full paper on WWW)
  6. B Rost & SI O'Donoghue: Sisyphus and prediction of protein structure, CABIOS, 1997, 13, 345-356. (full paper on WWW)
  7. B Rost and C. Sander, Bridging the protein sequence-structure gap by predictions?, Ann. Rev. Biophys. Biomol. Struc., 1996, 25, 113-136.
  8. B Rost & C Sander, Structure prediction of proteins - where are we now?, Cur. Opin. Biotech., 1994, 5, 372-380.
  9. B Rost & C Sander: Protein Structure Prediction by Neural Networks, in: M Arbib (ed.), The Handbook of Brain Theory and Neural Networks, Cambridge, MA: Bradford Books/The MIT Press, 1995, 772-775.
     

  10. A Lupas; M Van Dyke & J Stock: Predicting coiled coils from protein sequences. Science, 1991, 252, 1162-1164.
• WWW services for biologists
  1. B Rost & A Valencia: Pitfalls of protein sequence analysis. Curr. Op. Biotechn., 7, 1996, 457-461. ( full paper on WWW )
  2. B Rost: Learning From Evolution To Predict Protein Structure. In: B. Olsson, D. Lundh, A Narayanam (eds.) 'Bio-Computing and Emergent Computation', Skövde, Sweden, Sep 1-2, 1997. World Scientific, 87 - 101. ( full paper on WWW )
  3. B Rost, C Sander & R Schneider: PHD - a mail server for protein secondary structure prediction. CABIOS, 1994, 10, 53-60.
     
  4. B Rost & R Schneider: Pedestrian guide to analysing sequence databases. In: K Ashman (ed.) "Core techniques in biochemistry", Heidelberg: Springer, 1998, in press. ( full paper on WWW )
  5. Commented list of WWW services for biologists
• Predictions of 1D structure
  1. B Rost: Better 1D predictions by experts with machines, Proteins, 1998, Suppl. 1, 192-197. (full paper on WWW)
  2. B Rost, R Casadio & P Fariselli: Refining neural network predictions for helical transmembrane proteins by dynamic programming. In: D States et al. (eds.) "The fourth international conference on Intelligent Systems for Molecular Biology (ISMB)", St. Louis, U.S.A., Jun, 1996, Menlo Park, CA: AAAI Press, 1996, 192-200.
  3. B Rost, R Casadio, P Fariselli & C Sander: Prediction of helical transmembrane segments at 95% accuracy. Protein Science, 1995, 4, 521-533.
  4. B Rost, & C Sander: Progress of 1D protein structure prediction at last. Proteins, 1995, 23, 295-300.
  5. B Rost & C Sander: 1D secondary structure prediction through evolutionary profiles. In: H Bohr & S Brunak (eds.) "Protein Structure by Distance Analysis", Amsterdam: IOS Press, 1994, 257-276.
  6. B Rost & C Sander: Secondary structure prediction of all-helical proteins in two states. Protein Engng, 1993, 6, 831-836.
  7. B Rost & C Sander: Improved prediction of protein secondary structure by use of sequence profiles and neural networks. PNAS, 1993, 90, 7558-7562.
  8. B Rost & C Sander: Jury returns on structure prediction. Nature, 1992, 360,540.
• Prediction-based threading
  1. B Rost, R Schneider & C Sander: Fold recognition by prediction-based threading. JMB, 270, 1997, 1-10. (full paper on WWW)
  2. B Rost: Fold recognition by merging 1D structure prediction and sequence alignments. Preprint, EMBL, Germany, PDG-6/95, 1996. ( full paper on WWW )
  3. B Rost: Fitting 1D predictions into 3D structures. In: H Bohr & S Brunak, (eds.) "Protein folds. A distance based approach", Boca Raton, Florida: CRC Press, 1995, 132-151.
• Alignment/HSSP:
  1. C Sander & R Schneider: The HSSP data base of protein structure-sequence alignments. Nucl. Acids Res., 1994, 22, 3597-3599.
• Evaluation and testing of 1D predictions:
  1. B Rost, & C Sander: Bridging the protein sequence-structure gap by structure predictions. Ann. Rev. of Biophys. and Biomol. Structure, 25, 1996, 113-136.
  2. B Rost, & C Sander: Progress of 1D protein structure prediction at last. Proteins, 1995, 23, 295-300.
  3. B Rost, C Sander & R Schneider: Progress in protein structure prediction? TIBS, 1993, 18, 120-123.

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