| Proteins are the workhorses of biomolecules and their function is affected by their structure and their structural
rearrangements during ligand entry, ligand binding and protein–protein interactions. Hence, the knowledge
of protein structure and, importantly, the dynamic behaviour of the structure are critical for
understanding how the protein performs its function. The predictions of the structure and the dynamic behaviour
can be performed by combinations of structure modelling and molecular dynamics simulations.
The simulations also need to be sensitive to the constraints of the environment in which the protein resides.
Standard computational methods now exist in this field to support the experimental effort of solving protein
structures. This review presents a comprehensive overview of the basis of the calculations and the wellestablished
computational methods used to generate and understand protein structure and function and
the study of their dynamic behaviour with the reference to lung-related targets. |