Molecular Docking and 3D-QSAR Studies

The most important requirement for CoMFA and CoMSlA studies is that the 3D structures to be analyzed are aligned according to a suitable conformational template, which is assumed to be a bioactive conformation. To make the 3D-QSAR predicting models more relevant to the real active site of the enzyme, a flexible molecular docking approach was carried out. The docking conformations were assumed to be the actual bioactive binding conformations. 

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Hu, X., Stebbins, C. E. Molecular Docking and 3D QSAR Studies of Yersinia Protein Tyrosine Phosphatase YopH Inhibitors. Bioorg. Med. Chem. 2005, 13, 1101-1109. 

Hu X, Stebbins CE. Molecular docking and 3D-QSAR studies of Yersinia protein tyrosine phosphatase YopH inhibitors. Bioorg. Med. Chem. 2005 13 1101-1109. 

Tervo, A. J., Nyroenen, T. H., Ronkko, T., Poso, A. A Structure-Activity Relationship Study of Catechol-O-methyltrans-ferase Inhibitors Combining Molecular Docking and 3D QSAR Methods. 

Sekhar YN, Nayana MR, Sivakumari N et al (2008) 3D-QSAR and molecular docking studies of 1, 3, 5-triazene-2, 4-diamine derivatives against r-RNA novel bacterial translation inhibitors. J Mol Graph Model 26 1338-1352... 

Computed lipophilicity terms can be applied to structure—aaivity relationship studies. Here, the latest developments are the use of the molecular lipophilicity potential in three-dimensional quantitative structure—activity relationship (3D-QSAR) and docking studies. 

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