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In the next step, the C or 5 mC bismonophosphate molecule was manually docked to each of the starting structures.
Next, a padlock probe containing a transcript-specific barcode sequence is docked to each ODN and circularized in situ to form a single-stranded DNA circle.
Specifically, the molecules in the NCI Diversity Set I were docked to each protein in the protein database.
Then, a potentially interesting small molecule is docked to each element of the target database by a docking program.
CPT was docked to each β-CD derivative in the target database by two different docking programs, AutoDock 3.05 (Morris et al. 1998) and GlamDock 1.0 (Tietze and Apostolakis 2007).
PBs and SGs are often detected docked to each other, and it has been suggested that mRNAs can move between these two compartments [9].
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Each decoron model was manually docked to within 5 Å of each collagen binding site on the different receptor surfaces.
In docking-based IVS, a given small molecule is docked to the binding site of each protein in a target database through a docking engine.
Each compound was docked to the protein complex binding pocket, and a score from the docking was assigned to each compound according to the weighed component of the ICM scoring function (see below).
Given this, each analog was docked to the glmS riboswitch in dianionic form.
Each peptide library was docked to the ETS monomer conformations obtained from the clustering.
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