Protein kinases catalyze protein phosphorylation reactions, i.e. the transfer of the γ-phosphoryl group of ATP to tyrosine, serine and threonine residues of protein substrates. This phosphorylation plays an important role in regulating various cellular processes. Deregulation of many kinases is directly linked to cancer development and the protein kinase family is one of the most important targets in current cancer therapy regimens. This relevance to disease has stimulated intensive efforts in the biomedical research community to understand their catalytic mechanisms, discern their cellular functions, and discover inhibitors. With the advantage of being able to simultaneously define structural as well as dynamic properties for complex systems, computational studies at the atomic level has been recognized as a powerful complement to experimental studies. In this work, we employed a suite of computational and molecular simulation methods to (1) explore the catalytic mechanism of a particular protein kinase, namely, epidermal growth factor receptor (EGFR); (2) study the interaction between EGFR and one of its inhibitors, namely erlotinib (Tarceva); (3) discern the effects of molecular alterations (somatic mutations) of EGFR to differential downstream signaling response; and (4) model the interactions of a novel class of kinase inhibitors with a common ruthenium based organometallic scaffold with different protein kinases. Our simulations established some important molecular rules in operation in the contexts of inhibitor-binding, substrate-recognition, catalytic landscapes, and signaling in the EGFR tyrosine kinase. Our results also shed insights on the mechanisms of inhibition and phosphorylation commonly employed by many kinases.