KUPS - Test Set

KUPS Test Set Collection

Predicting Protein-Protein Interaction

  • Bader, G. D., D. Betel, et al. (2003). "BIND: the Biomolecular Interaction Network Database." Nucleic Acids Res 31(1): 248-250.

  • Browne, F., H. Wang, et al. (2009). "GRIP: A web-based system for constructing Gold Standard datasets for protein-protein interaction prediction." Source Code Biol Med 4: 2.

  • Chen, X. W. and M. Liu (2005). "Prediction of protein-protein interactions using random decision forest framework." Bioinformatics 21(24): 4394-4400.

  • Guo, Y., L. Yu, et al. (2008). "Using support vector machine combined with auto covariance to predict protein-protein interactions from protein sequences." Nucleic Acids Res 36(9): 3025-3030.

  • Park, Y. (2009). "Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences." BMC Bioinformatics 10: 419.

  • Pitre, S., F. Dehne, et al. (2006). "PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs." BMC Bioinformatics 7: 365.

Predicting Protein Function

  • Guldener, U., M. Munsterkotter, et al. (2005). "CYGD: the Comprehensive Yeast Genome Database." Nucleic Acids Res 33(Database issue): D364-368.

Predicting Protein Interface Residues

  • Chen, X. W. and J. C. Jeong (2009). "Sequence-based prediction of protein interaction sites with an integrative method." Bioinformatics 25(5): 585-591.