Ramachandran then spent two years (1947–1949) at the Cavendish Laboratory in Cambridge, where he earned his Ph.D. for 'studies on X-ray diffuse scattering and its application to determination of elastic constants'.
Wanting to tackle problems at a more fundamental level, Ramachandran decided to use this information to examine the various polypeptide conformations then known and also to develop a good 'yardstick' that could be used for examining and assessing any structure in general, but peptides in particular. The result which emerged from these calculations in 1962, - now commonly known as the Ramachandran plot - was published in the Journal of Molecular Biology in 1963 and has become an essential tool in the field of protein conformation. When it was first calculated, crystal structures had barely been obtained for any protein. From the mid 1960s onward Ramachandran studied many topics relating to the conformation of peptides including types of β-turns, conformation of prolyl residues, cis-peptide units, occurrence and need for non-planarity of the peptides, NMR coupling constants, peptides containing L and D residues and many others.
Ramachandran can be credited for bringing together into the one field of molecular biophysics the then disparate fields of X-ray crystallography, peptide synthesis, NMR and other optical studies, and physico-chemical experimentation.
In 1970 he founded the Molecular Biophysics Unit at the Indian Institute of Science which was later known as the Centre of Advanced Study in Biophysics and Crystallography.
Ramachandran and A.V. Lakshminarayana developed convolution-backprojection algorithms which greatly improved the quality and practicality of results obtainable by x-ray tomography. Compared to previously used methods, their algorithms considerably reduced computer processing time for image reconstruction, as well as providing more numerically accurate images. As a result, commercial manufacturers of x-ray tomographic scanners started building systems capable of reconstructing high resolution images that were almost photographically perfect. In 1971, they published their research in a paper (“Three dimensional reconstructions from radiographs and electron micrographs: Application of convolution instead of Fourier Transforms,” Proc. Nat. Acad. Sci., vol. 68, pp. 2236-2240, 1971).
Notable awards that Ramachandran received include the Shanti Swarup Bhatnagar Award for Physics in India and the Fellowship of the Royal Society of London. In 1999 the International Union of Crystallography honored him with the Ewald Prize for his 'outstanding contributions to crystallography'.