might be illustrator or any other vector drawing software, or else a 3D program, such as Blender. If you post an example of what you want to achieve it'd be easier to point in the right direction.
As Eugenio pointed out, the author is using a vector drawing software (CorelDraw, Illustrator, Inkscape) to draw the proteins and a 2D Chemical Drawing Software (like MarvinSketch, ChemDoodle or ChemOffice) to draw the molecules. It is easier to start from a model generated by a good 3D modeling software (I'd like to recommend UCSF Chimera) and then use your vector drawing software to tweak and improve your graphic.
Your question is very interesting as to what programs to use for such type of layout, unfortunately you have to use several programs and a lot of them are proprietary license. However there are alternatives, although it is difficult to lay out very complex chemical structures in latex, you can look at the following link:
Many thanks to all of you who have sent me an answer. I'm not used to drawing or using these programs. I'll study about it and try to get the software, if possible, and use it.