Iowa State University
Plant Sciences Institute

Laurence H. Baker Center for Bioinformatics and Biological Statistics


CDM PROTEIN SECONDARY STRUCTURE PREDICTION SERVER

GOR V Secondary Structure Prediction Server
 

Introduction:

In order to improve the accuracy of secondary structure predictions, we propose a new hybrid method: Consensus Data Mining (CDM). CDM combines our two previous successful secondary structure prediction methods:
  • Fragment Database Mining (FDM) (Cheng et al., 2005), and
  • GOR V (Kloczkowski et al., 2002;Sen et al., 2005).
The basic premise of CDM is that the combination of these two complementary methods can enhance the performance of the overall secondary structure prediction by harnessing the distinct advantages both methods afford:
  • FDM exploits the availability of sequentially similar fragments in the PDB, which leads to highly accurate (much better than GOR V) prediction of structure for such fragments, but such fragments are not available for many cases.
  • GOR V predicts the secondary structure of less similar fragments fairly accurately, where usually the FDM method does not find suitable structures.
Please refer to the papers in the bottom of the page for more information.


CDM Secondary Structure Server:

Sequence name (optional):

Your e-mail address :

Paste a protein sequence below:
(Please use one-letter amino acid codes with no comment line--the submission is limited to 1000 residues)


References for CDM:

* Sen, T.Z., Cheng, H., Kloczkowski, A., Jernigan, R.L. "A Consensus Data Mining
secondary structure prediction by combining GOR V and Fragment Database Mining",
Protein Sci. 15(11):2499-2506, 2006. pdf

References for FDM:

*Cheng, H., Sen, T.Z., Kloczkowski, A., Margaritis, D., Jernigan, R.L., "Prediction of
protein secondary structure by mining structural fragment database", Polymer 46,
4314- 4321, 2005. pdf

References for GOR V:

* Kloczkowski, A., Ting, K.-L, Jernigan, R.L., Garnier, J., "Combining the
GOR V algorithm with evolutionary information for protein secondary
structure prediction from amino acid sequence", Proteins, 49, 154-166, 2002. pdf

* Sen, T.Z., Jernigan, R.L., Garnier, J., Kloczkowski, A., "GOR V server for
protein secondary structure prediction", Bioinformatics, 21(11), 2787-2788,
2005.
pdf

General References for GOR:

* Garnier, J., Osguthrope, D.J., Robson, B. J. Mol. Bio., 130, 97-120, 1978.
* Gibrat, J.F., Garnier, J., Robson, B. J. Mol. Bio., 198, 425-443, 1987.
* Garnier, J., Gibrat, J.F., Robson, B. Methods Enzymol., 266, 540-553, 1996.
* Kloczkowski, A., Ting, K.-L, Jernigan, R.L., Garnier, J. Polymer, 43, 441-449, 2002.

Please refer your questions/comments about this server to Taner Z. Sen from the Jernigan group.