Assessing search strategies for flexible docking

Vieth, Michał; Hirst, Jonathan D.; Dominy, Brian N.; Daigler, Heidi; Brooks, Charles L.

doi:10.1002/(sici)1096-987x(19981115)19:14<1623::aid-jcc8>3.0.co;2-l

Cited by 113 publications

(119 citation statements)

References 23 publications

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“…com) platform. [15][16][17] The docking results are reported energy as score. It means that the higher score indicates the more favorable docking model.…”

Section: Methodsmentioning

confidence: 99%

Darapladib Binds to Lipoprotein-Associated Phospholipase A2 with Meaningful Interactions

Rok¹,

Kim

Chang

et al. 2014

Bulletin of the Korean Chemical Society

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Lipoprotein-associated phospholipase A2 (Lp-PLA 2 ) is a crucial enzyme in atherosclerosis as a potential drug target. The most remarkable Lp-PLA 2 inhibitory drug is Darapladib. We determined the binding pose of Darapladib to Lp-PLA 2 through docking study. Darapladib formed two hydrogen bonding interactions with the side chain of Tyr160 and Gln352 and several pi-pi interactions with aromatic and aliphatic hydrophobic residues of Lp-PLA 2 . It is known that the dietylpropan-amine moiety of Darapladib has influence on the improvement of its oral bioavailability and we supposed this in our docking results.

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“…com) platform. [15][16][17] The docking results are reported energy as score. It means that the higher score indicates the more favorable docking model.…”

Section: Methodsmentioning

confidence: 99%

Darapladib Binds to Lipoprotein-Associated Phospholipase A2 with Meaningful Interactions

Rok¹,

Kim

Chang

et al. 2014

Bulletin of the Korean Chemical Society

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“…[15][16][17] This algorithm assumes a rigid protein and permits only the ligand to be flexible. Input Site Sphere parameter specifies a sphere around the center of the binding site, where the CDOCKER experiment is to be performed.…”

Section: Methodsmentioning

confidence: 99%

3',4'-Dihydroxyl Groups in Luteolin are Important for Its Inhibitory Activities against ADAMTS-4

Choi¹,

Jeong²,

Kim³

et al. 2012

Bulletin of the Korean Chemical Society

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A disintegrin and metalloprotease with thrombospondin domains (ADAMTS) are a member of peptidase and involved in processing of von Willebrand factor as well as cleavage of aggrecan, versican, brevican and neurocan. Among 19 subfamilies of human ADAMTS, ADAMTS-4 is a zinc-binding metalloprotease and is a famous therapeutic target for arthritis. It has been reported that a flavonoid luteolin shows inhibitory activity against ADMATS-4. In this study, we verified that luteolin is a potent inhibitor of ADAMTS-4 and probed the molecular basis of its action. On the basis of a docking study, we proposed a binding model between luteolin and ADAMTS-4 in which 3',4'-dihydroxyl groups in luteolin formed hydrogen bonding with ADMATS-4 and these interactions are important for its inhibitory activity against ADAMTS-4.

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“…Vieth et al [21] presented an ad hoc "efficiency" measure to evaluate the success of docking. Most methods judge success by conformations that are within a given tolerance, typically 1 to 1.5 A RMSD away from the crystallographic structure.…”

Section: Testing and Evaluating Docking Methodsmentioning

confidence: 99%