Home
Index

 BIGS


 Software


Workshop


Others

Protein Secondary Structure Prediction (PSSP)

DATA

ProteinData - Protein Data Base. Each protein is represented by its sequence of amino acids and distances between them.

CODE

SourceCode - Java Source Code for the protein data treatment.

BIBLIOGRAPHY

  • 1. Fariselli, P., Casadio, R., 1999. A neural network based predictor of residue contacts in proteins. Protein Engineering, Vol. 12, No. 1, 15-21.
  • 2. Fariselli, P., Olmea, O., Valencia, A., Casadio, R., 2001. Prediction of contact maps with neural networks and correlated mutations. Protein Engineering. 14(11):835-843.
  • 3. Guo, L., Huang, D.S., Zhao, W., 2003. Combining genetic optimisation with hybrid learning algorithm for radial basis function neural networks. IEE Electron. Lett. 39 (22), 1600–1601.
  • 4. Guo, J., Chen, H., Sun, Z., Lin, Y., 2004. A novel method for protein secondary structure prediciton using dual-layer SVM and profiles. Proteins: Struct. Funct. Bioinform. 54, 738–743.
  • 5. Huang, D.S., 1999. Radial basis probabilistic neural networks: Model and application. Int. J. Pattern Recognit. Artif. Intell. 13 (7), 1083–1101.
  • 6. Olmea, O., Rost, B., Valencia, A., 1999. Effective use of sequence correlation and conservation in fold recognition. J. Mol. Biol. 293, 1221–1239.
  • 7. Pollastri, G., Baldi, P., 2002. Prediction of contact maps by recurrent neural network architectures and hidden context propagation from all four cardinal corners. Bioinformatics 18 (Suppl.), S62–S70.
  • 8. Vullo, A., Walsh, I., Pollastri, G., 2006. A two-stage approach for improved prediction of residue contact maps. BMC Bioinformatics 7, 180.
  • 9. Zhang, G.-Z., Huang, D.S., 2004. Prediction of inter-residue contacts map based on genetic algorithm optimized radial basis function neural network and binary input encoding scheme. J. Comput. Aided Mol. Des. 18, 797–810.
  • 10. Zhang, G.-Z., Huang, D.S., 2005. Combing a binary input encoding scheme with RBFNN for globulin protein inter-residue contact map prediction. Pattern Recognit. Lett. 26, 1543–1553.
  • 11. Walsh, I., Bau, D., Martin, A. JM., Mooney, C., Vullo, A., Pollastri, G., 2009. Ab initio and template-based prediction of multi-class distance maps by two-dimensional recursive neural networks. BMC Structural Biology. 9:5.
  • 12. Bohr, H., Bohr, J., Brunak, S., Cotterill, RM., Lautrup, B., Nørskov, L., Olsen, OH., Petersen, SB., 1988. Protein secondary structure and homology by neural networks. The alpha-helices in rhodopsin. FEBS Lett. 1988 Dec 5;241(1-2):223-8.
  • 13. Bohr, H., Bohr, J., Brunak, S., Cotterill, R.M.J, Fredholm, H., Lautrup, B., 1990. A novel approach to prediction of the 3-dimensional structures of protein backbones by neural networks. FEBS Letters 261 (1990), pp. 43–46.