Our lab is interested in understanding at the molecular level the mechanisms of protein-protein interactions and its implications in the whole system response. We focus on the mitogen-activated protein kinase(MAPKs) signal transduction pathway. MAPKs are a family of serine/threonine kinases that play an essential role in signal transduction by modulating gene transcription in the nucleus in response to changes in the cellular environment. MAPK signaling modules have been conserved throughout evolution, from plants, fungi, nematodes, insects, to mammals. Their ubiquity and versatility raise the issue of how they achieve specific coupling of signal to cellular response. How do the kinases in the cascade along with scaffold protein assembly to transmit the signal? How the signal is modulated by the mechanisms of protein-protein interactions? How MAP kinases achieve specificity by differential recognition between their substrates and regulators? How unstructured transcription factors recognize their targets? In order to answer these and other questions we apply computational tools that allow us to study MAPKs at the molecular and systems biology level. We use and develop tools such as: Quantum Mechanics/Molecular Mechanics to study reaction mechanisms, Molecular dynamics to understand protein flexibility, docking methods to describe protein-protein complexes, network modeling to understand the cascade response, structural databases and data mining to classify and characterize protein structure.