Recent technological advances in protection, control and optimization are enabling a more automated power system. Research efforts are focused on integrating these technologies into a seamless and cyber secure infrastructure for protection, control and operation. This infrastructure is the basis for accommodating and providing robust solutions to new problems arising from the integration of renewables, increased uncertainty and steeper ramp rates. The system must be secure against malicious cyber-attacks at every level. We discuss the infrastructure at the substation level where we build upon the dynamic state estimation based protection (EBP) and a centralized substation protection integrated with distributed dynamic state estimation and all substation control, operation and optimization functions. All functions are model based: we discuss an automated creation of the models required at each level of a hierarchical control, operation and optimization functions. The substation level system is extended to a subsystem/agent level for control and optimization at subsystems consisting of extended clusters of substations. At subsystem level, the infrastructure enables full state feedback for optimal control. Issues of time latency are addressed. Finally, the concepts are extended to the control center where all the functions that coordinate substations and subsystems are exercised. At each one of the three levels (substation, subsystem, control center), defenses against malicious cyber-attacks are integrated. We will discuss data attacks as well as insertion of malicious commands and the integrated intrusion detection methods. The proposed approach and infrastructure forms the basis for the next generation of Energy Management Systems.