PDG. CNB-CSIC. Contact Prediction Server. Help

Contact Prediction Server. Help

[Contributors] [Protein Design Group @ CNB-CSIC] [Predicted pairs format] [References] [Contact]

This server takes as input a single sequence, in ReadSeq compatible format, and predicts contacts between residues in the three-dimensional structure of the protein.

Contact predictions are base on "correlated mutations" (refs.) and tree-determinat (refs.) residues. Contacts among hydrophobic and conserved residues can be also reported (to be used as a base-line for predictions, for example).

For the calculation of correlated mutations, tree-determinants and conserved residues a multiple sequence alignment is built in the following way:

BLAST (refs.) is used to search for homologous proteins in a non-redundant database.
CLUSTALW (refs.) is used to align those homologous sequences.
The alignmet is filtered to avoid redundance: if two sequeces have homology over a given value, one of them is eliminated.
Divergent sequences (very distant homologous) are eliminated.
Small fragments are also eliminated from the alignment.

Contributors

O. Olmea. For the research on correlated mutations carried out in the group.
J. M. Fernandez and F. Abascal. For setting up the BLAST system and for maintaining the databases.
F. Abascal. For the program used to retrieve sequences by ID.

Pairs format

CLASIC. The format used by the programs developed in our group.
Example:

   3    9    x       x       V   I  xx  xx   -0.0165
   3   10    x       x       V   K  xx  xx    0.0164
   3   11    x       x       V   C  xx  xx   -0.1332
   3   12    x       x       V   K  xx  xx    0.0077
   3   16    x       x       V   C  xx  xx   -2.0000
   3   17    x       x       V   V  xx  xx    0.0897
   3   18    x       x       V   E  xx  xx    0.0186
   3   19    x       x       V   V  xx  xx    0.0630

PDG. The format used by our server for evaluation of contact prediction. More information about this format.
Example:

    3     6 A L      0.212
  100   106 D H      0.934
   25   100 R D      1.054
    3    15 A D      0.635
   23    40 R D      1.054

CASP. The format used in the 4th meeting on the "Critical Assessment of Techniques for Protein Structure Prediction" ( CASP4). More information about this format.
Example:

  16   20   0   8   1.000
  16   21   0   8   1.000
  16   39   0   8   1.000
  16   42   0   8   1.000
  16   45   0   8   1.000
  16   49   0   8   1.000
  16   53   0   8   1.000
  20   21   0   8   1.000
  20   39   0   8   1.000
  20   42   0   8   1.000
  20   45   0   8   1.000

References

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. (1997). Nucleic Acids Res. Sep 1; 25(17):3389-402. Review.
Thompson, J. D., Higgins, D. G. and Gibson, T. J. (1994). CLUSTALW: improving the sensitivity of progresive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acid Res., 22, 4673-4680.
Göbel, U., Sander, C., Scheneider, R., Valencia, A. (1994). Correlated mutations and residue contacts in proteins. Proteins 18:309-317.
Olmea O, Valencia A (1997) Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Folding & Design 2, S25-S32
Pazos, F., Helmer-Citterich, M., Ausiello, G., Valencia, A., (1997) Correlated Mutations Contain Information About Protein-Protein Interaction. J. Mol. Biol , 271(4):511-523.
Pazos, F., Olmea, O. and Valencia, A.(1997). A graphical interface for correlated mutations and other structure prediction methods. CABIOS. 13(3):319-321.
Casari, G. Sander, C., Valencia, A. (1995) A method to predict functional residues in proteins. Nature S. B. 2: 171-178.
Casari, G., Sander, C., Valencia, A. (1995) Sequencespace. In "Protein Fold: A distance based approach" Ed. H. Bohr, S. Brunak. CRC Press Inc.
Andrade M A, Casari G, Sander C, Valencia A (1997) Classification of protein families and detection of the determinat residues with a self-organizing neural network. Biol. Cybern. 76, 441-450.
Pazos F, Sanchez-Pulido L, García-Ranea J A, Andrade M A, Atrian S, Valencia A (1997). Comparative analysis of different methods for the detection of specificity regions in protein families. In D. Lundh. Olsson, B, Narayanan, A. (Eds.), Biocomputing and Emergent Computation (pp. 132-145). Singapore, New Jersey, London, Hong Kong: World Scientific.
Olmea O, Rost B, Valencia A. (1999). Effective use of sequence correlation and conservation in fold recognition. J Mol Biol. 293(5):1221-1239.

Contact us

Florencio Pazos & Alfonso Valencia
Protein Design Group
National Center for Biotechnology (Spanish Research Council)
Campus Universidad Autonoma.
Cantoblanco. 28049 Madrid.
Tlf: +34-91-5854669. Fax: +34-91-5854506.