Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions. Export

@article{citeulike:2269884, abstract = {In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors.}, address = {Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Queen Rania Street, Amman 11942, Jordan.}, author = {Abu Hammad, A. M. and Afifi, F. U. and Taha, M. O.}, citeulike-article-id = {2269884}, citeulike-linkout-0 = {http://dx.doi.org/10.1016/j.jmgm.2007.02.002}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/17360207}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=17360207}, doi = {10.1016/j.jmgm.2007.02.002}, issn = {1093-3263}, journal = {J Mol Graph Model}, keywords = {combination, docking, qsar}, month = {September}, number = {2}, pages = {443--456}, posted-at = {2008-01-21 19:54:49}, priority = {2}, title = {Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions.}, url = {http://dx.doi.org/10.1016/j.jmgm.2007.02.002}, volume = {26}, year = {2007} }

TY - JOUR ID - citeulike:2269884 L3 - citeulike-article-id:2269884 N2 - In this project, several docking conditions, scoring functions and corresponding protein-aligned molecular field analysis (CoMFA) models were evaluated for a diverse set of neuraminidase (NA) inhibitors. To this end, a group of inhibitors were docked into the active site of NA. The docked structures were utilized to construct a corresponding protein-aligned CoMFA models by employing probe-based (H+, OH, CH3) energy grids and genetic partial least squares (G/PLS) statistical analysis. A total of 16 different docking configurations were evaluated, of which some succeeded in producing self-consistent and predictive CoMFA models. However, the best model coincided with docking the ionized ligands into the hydrated form of the binding site via PLP1 scoring function (r2LOO=0.735, r2PRESS against 24 test compounds=0.828). The highest-ranking CoMFA models were employed to probe NA-ligand interactions. Further validation by comparison with a co-crystallized ligand-NA crystallographic structure was performed. This combination of docking/scoring/CoMFA modeling provided interesting insights into the binding of different NA inhibitors. IS - 2 JF - J Mol Graph Model SN - 1093-3263 AD - Department of Pharmaceutical Sciences, Faculty of Pharmacy, University of Jordan, Queen Rania Street, Amman 11942, Jordan. EP - 456 TI - Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions. VL - 26 SP - 443 KW - combination KW - docking KW - qsar AU - Abu Hammad, AM AU - Afifi, FU AU - Taha, MO PY - 2007/09// UR - http://dx.doi.org/10.1016/j.jmgm.2007.02.002 ER -