Sentence examples for default conformation from inspiring English sources
For AutoDock Vina, the default conformation search algorithm, which is a combination of optimization algorithms, including genetic algorithms, particle swarm optimization, and simulated annealing, and the default scoring function, which is a hybrid score function derived from the X-score, are used.
If the calculated RMSD value is smaller than or equal the specified cut-off, which is 1.0 by default, that conformation is added to the 'bin' containing the best conformation.
After all, the current PubChem3D theoretical conformer generation approach does not guarantee that the single (default) conformer used for each molecule in the NN pairs is a (or "the") bioactive conformation.
In-house program Cyndi [38, 39], which uses a multi-objective evolution algorithm method for conformer searching, was chosen by default to generate multiple conformation.
In a first approach, we have used a default voting system: the conformations are ranked according to the number of + marks they have received.
No filters were set and default constraints were applied to the ligand conformation generation procedure to yield a broad range of conformations and stereoisomers.
A multiconformer library was generated using Cyndi with the default settings (up to 200 conformers per a compound), resulting in a library of 2,735,015 conformations.
In the default setting, PharmDock uses the ligand conformations generated by OpenEye Omega [12 14] as docking input.
The conformational models of the different query molecules were calculated using omega (default settings, with a maximum of 400 conformations per molecule).
Subsequently, conformations of the cationic ligands were generated using a systematic search method in MOE that was adjusted for large chemical databases (conformation import function) using the default settings.
Docked complexes between the highest-ranked peptides and the 12 protein conformations were analysed using HBPLUS, using default parameters [50].
