Computational docking studies

Given the multitude of approaches now used to dock small molecules and peptides to proteins, why should the protein-protein docking problem require its own approaches Could one make do with the software packages developed for these related problems Unfortunately, the answer is usually no. 

Another difference between protein-protein and protein-small-molecule docking involves the treatment of nonbonded interactions. For the docking of rigid low molecular weight compounds, the receptor s molecular interaction 

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It must be mentioned that to understand the stereochemical outcome of the reaction a detailed mechanistic analysis turns out to be critical, not only to determine the binding mode in the active site and the stereochemistry of the addition, but also to identify which of the EWGs acts as the activating one. In different instances, it has been done by either deuterium labeling experiments [122,123] or computational docking studies [37]. 

Wolohan, P., Reichert, D.E. CoMFAand Docking Study of Novel Estrogen Receptor Subtype Selective Ligands. J. Comput.-Aided Mol Des. 2003, 27, 313-328. 

Another conformation different from T-taxol was proposed based on molecular dynamics simulations and computational docking restrained by the two REDOR distances [85], The main difference between this conformer (named REDOR-taxol or PTX-NY) and T-taxol is the conformation of the C13 side chain, that places the 2 -OH in a different orientation. However, subsequent studies demonstrated that PTX-NY is not consistent with the EC density [86, 87],... 

Desiraju GR, Gopalakrishnan B, Jetti RKR, Nagaraju A, Raveendra D, Sarma JARP, et al. Computer-aided design of selective COX-2 inhibitors Comparative molecular field analysis, comparative molecular similarity indices analyses, and docking studies of some 1,2-diarylimidazole derivatives. J Med Chem 2002 45 4847-57. 

Wolohan P, Reichert DE. CoMFA and docking study of novel estrogen receptor subtype selective ligands. J Comput Aided Mol Des 2003 17 313-28. 

Masetti M, Cavalli A, Recanatini M (2008) Modeling the hERG potassium channel in a phospholipid bilayer molecular dynamics and drug docking studies. J Comput Chem 29(5) 795-808... 

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