Today, protein structure is mainly predicted by aligning the unknown amino acid sequence against all sequences for which we already know the physical structure. Whilst sequences differing in length can be readily catered for by inserting or deleting (with or without affine gap penalties) the odd amino acid, there will frequently be cases where there are mutations. To compensate for this, the likes of the BLOSUM matrix is used to score the likelihood of one amino acid having mutated into another. For example, a hydrophobic residue is more likely to be swapped for something similar, than it is to be replaced with something strongly hydrophilic.
Whilst this is an entirely reasonable basis, there are many other physical property factors which which can be considered. In fact, the Amino Acid Index currently lists 544 physicochemical and biochemical properties of amino acids. A paper by Yi He et al. PNAS 2015;112:5029-5032 recently made use of a subset of these properties to predict structure. Their work shown below shows target T0797 (B) from CASP 11 compared with a purely physical structure predicted using their method (A) and the PSI BLAST candidate for the same sequence (C).
Even though their structure only had three residues in common with the target sequence, it is plainly more similar than the PSI BLAST attempt. The RMSD between structures A and B is also reported as being 0.73 Å, whilst PSI BLAST returns an RMSD of 2.09 Å.