SPADAN: A Novel Strategy for Dynamic Modeling of Protein-Protein Interaction Networks
Researchers have unveiled a groundbreaking strategy named the Systematic Protein Association Dynamic ANalyzer (SPADAN), designed to automatically convert protein-protein interaction (PPI) networks into genome-wide dynamic models. This innovative pipeline begins with the construction of a PPI network based on a specified list of proteins, which is then translated into the comprehensive language of biochemical reactions, incorporating essential chemical details.Following this translation, a series of ordinary differential equations (ODEs) are generated to describe the kinetics of these reactions. To enhance the model's accuracy, SPADAN employs a large-scale and distributed parameter approximation algorithm that estimates system parameters using high-throughput time-series experimental data.This novel approach not only provides a holistic view of protein interactions but also enables quantitative predictions of system behavior, making it a valuable tool for understanding the dynamics of molecular interactions. The applicability of SPADAN has been demonstrated through modeling protein interactions in colorectal cancer, offering insights that could inform therapeutic interventions in precision medicine.
Developers: Pooya Borzou, Jafar Ghaisari, Iman Izadi, Yasin Eshraghi, Yousof Gheisari
