Presently it is not possible to know the folded 3-D structure of a protein from the amino acid sequence unless the amino acid sequence is very similar to an already known structure. However a technique to understand and discover the 3-D structure of various proteins is called x-ray crystallography.
A beam of x-ray is directed towards a crystal of the desired protein and the x-ray is diffracted in certain spots revealing the protein's 3-D structure. But in recent years, finding a suitable crystal has become the slowest step of the procedure. A crystal requires huge amounts of pure protein and searching for the perfect conditions takes years. Also many proteins, more specifically membrane proteins, have resisted attempts to crystallize them.
This unique kind of method has been able to solve ribosomal structures which contains over 50 proteins. With more uses of this method scientists will be able to easily determine the structure of a complex protein by simply shining a beam of light into its crystal form.
Alberts, Bruce. “Analyzing Protein Structure and Function.” Molecular Biology of the Cell. 4th Edition., U.S. National Library of Medicine, 1 Jan. 1970, www.ncbi.nlm.nih.gov/books/NBK26820/.