Introduction to distanceP
This server is an update and improvement of the
sowhat server.
For an overview consult the abstracts of the
following papers (Abstract tab). 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 tab.
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.
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/)
