Protein, proteins binding site comparison

It is worth to mention that binding site comparison relies on the entries of the structural protein database. The increasing number of available crystal structures will facilitate the identification of similar binding sites and potential off-targets and is most suitable for large protein families like kinases or proteins with purine containing binding sites (93). 

Das S, Kokardekar A, Breneman CM (2009) Rapid comparison of protein binding site surfaces with property encoded shape distributions. J Chem Inf Model 49 2863-2872... 

Statistics including large and diverse sets of protein structures have revealed that the 20 amino acid residue types exhibit distinctly different levels of flexibility [138], Gin residues appear to be amazingly flexible (given their medium size) and are used in the following section for exemplifying some of the caveats that complicate binding site comparisons. 

Gold, N.D., Jackson, R.M. Fold independent structural comparisons of protein-Hgand binding sites for exploring functional relationships. J. Mol. Biol. 2006,355,1112-24. 

Weill, N. and Rognan, D. 2010. Alignment-free ultra-high-throughput comparison of druggable protein-ligand binding sites. /. Chem. Inf. Model. 50 123-135. 

Desaphy J, Azdimousa K, Kellenberger E, Rognan D (2012) Comparison and draggability prediction of protein-ligand binding sites from pharmacophore-annotated cavity shapes. J Chem Inf Model 52(8) 2287-2299... 

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