Laryngektomie

Glunz, Mechthild; Reuß, Cornelia; Schmitz, Eugen; Stappert, Hanne

doi:10.1007/978-3-662-08242-3

Cited by 1 publication

(1 citation statement)

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“…A subsequent literature analysis showed that most of the 30 decoys that score better than À25 kJ mol À1 either belong to known thrombin inhibitor classes or are even disclosed as thrombin inhibitors. [53][54][55][56] The 10 highest-scored decoys include thrombin inhibitors ZINC03807318 (À37 kJ mol À1 ), ZINC03807319 (À33 kJ mol À1 ), ZINC03842250 (À35 kJ mol À1 ), ZINC03838231 (À31 kJ mol À1 ), ZINC04633621…”

Section: Thrombinmentioning

confidence: 99%

Towards an Integrated Description of Hydrogen Bonding and Dehydration: Decreasing False Positives in Virtual Screening with the HYDE Scoring Function

et al. 2008

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We developed a new empirical scoring function, HYDE, for the evaluation of protein-ligand complexes. HYDE estimates binding free energy based on two terms for dehydration and hydrogen bonding only. The essential feature of this scoring function is the integrated use of log P-derived atomic increments for the prediction of free dehydration energy and hydrogen bonding energy. Taking the dehydration of atoms within the interface into account shows that some atoms contribute favorably to the overall score, while others contribute unfavorably. For instance, hydrogen bond functions are penalized if they are dehydrated unless they can overcompensate this loss by forming a hydrogen bond with excellent geometry. The main stabilizing contribution represents the removal of apolar groups from the water: the hydrophobic effect. Initial studies using the DUD dataset show that with HYDE, there is a significant decrease in false positives, a reasonable categorization of compounds as either non-binders, weak, medium or strong binders, and in particular, there is a generally applicable and thermodynamically sensible cutoff score below which there is a high likelihood that the compound is indeed a binder.

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Section: Thrombinmentioning

confidence: 99%