Membrane proteins (MPs) are abundant important functional proteins and as such they represent more than 60% of drug targets. However, experimentally, the fine characterisation of their structure and function is made difficult by the environment in which they are embedded. Dedicated bioinformatics methods and specific molecular simulations approaches are thus required to gain relevant information. I will discuss recent progresses made in our team in the development of structural bioinformatics methods for MPs. I will also illustrate the power and limits of molecular dynamics simulations to explore transport properties and conformational changes of MPs