CBS-DK
distanceP

Introduction


CPHmodels:
Homology modelling of proteins


distanceP
Prediction of distances in proteins
(Sowhat update)


RedHom:
Reduction of sequence similarity in a data set


Introduction to distanceP

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This server is an update and improvement of the sowhat server. For an overview consult the abstracts of the following papers. Detailed background and introduction can be found in the papers:
  • Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. J. Gorodkin, O. Lund, C. A. Andersen, and S. Brunak. In proceedings of the seventh international conference for molecular biology, eds. T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H-W. Mewes, and R. Zimmer, pp 95-105, 1999. (http://www.cbs.dtu.dk/services/distanceP/)

  • Protein distance constraints predicted by neural networks and probability density functions. O. Lund, K. Frimand, J. Gorodkin, H. Bohr, J. Bohr, J. Hansen, and S. Brunak. Protein Engineering, Volume 10, Issue 11: November 1997. 1241-1248. (http://www.cbs.dtu.dk/services/CPHmodels/)
  • Download the transparancies from the talk given at ISMB'99.

    Download the poster presented at BIOINFORMATICS'99.

    A description of distanceP is given on the Manual page.

    For each sequence separation (residues) a threshold has been computed as the average physical distance (Angstrom) with sequence windows chosen from a non-redundant data set of proteins with known three-dimensional structure. Each of these thresholds serves as constraints for the neural network predictions. The networks predict whether the physical distance for two sequence separated residues is below or above the thresholds. The computed thresholds for each sequence separation can be downloaded here. The list of pdb entries that were used for training the neural networks in distanceP can be downloaded here.
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    Paper to reference when reporting results

    Using Sequence Motifs for Enhanced Neural Network Prediction of Protein Distance Constraints. J. Gorodkin, O. Lund, C. A. Andersen, and S. Brunak. In proceedings of the seventh international conference for molecular biology, eds. T. Lengauer, R. Schneider, P. Bork, D. Brutlag, J. Glasgow, H-W. Mewes, and R. Zimmer, pp 95-105, 1999. (http://www.cbs.dtu.dk/services/distanceP/)

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    Problems, comments and suggestions: Jan Gorodkin 

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