1) Ruiz-Blanco, Y. B., Marrero-Ponce, Y., Paz, W., Green, J.R., "ProtDCal-v1: A Protein Descriptor Generator Software for Data Mining Applications." In preparation.
2) Ruiz-Blanco, Y. B., Marrero-Ponce, Y., Paz, W., García, Y., & Salgado, J. (2013). "Global Stability of Protein Folding from an Empirical Free Energy Function". Journal of Theoretical Biology, 321, 44-53.
3) Ruiz-Blanco, Y. B., García, Y., Sotomayor-Torres, C. M., & Marrero-Ponce, Y. (2010). "New Set of 2D/3D Thermodynamic Indices for
Proteins. A Formalism Based on “Molten Globule” Theory." Physics Procedia, 8, 63-72.
Protein-protein interaction prediction engine (PIPE) v3b. Predicts PPIs based on co-occurance of short interaction-mediating protein sequences. Works for multiple species. Has been demonstrated to be the most accurate (highest precision/recall) when operating at high specificities (99.95%) required for high-throughput analysis.
Builds on our PIPE method to also predict the location of protein-protein interaction. More accurate than other contemporary methods when evaluated against experimental data from protein truncation studies (Domino dataset).
An open source genetic algorithms library for the STI Cell BE processor. Although the STI Cell BE processor is no longer widely used, this project was widely used and has been downloaded more than 500 times.