Publications by authors named "Yulia V Borodina"
We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med.
View Article and Find Full Text PDFThe size of conformational ensembles required for regular coverage of the conformational space of druglike molecules was examined. Using the conformer generation program Omega, the number of regularly distributed conformers (NRC) of flexible compounds was determined as a function of the root-mean-square deviation (RMSD) resolution of coverage. A regression equation was developed predicting the NRC of a molecule as a function of RMSD.
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- The PASS program has been applied to approximately 250,000 compounds from the NCI Open Database, leading to the integration of over 64 million predictions in the Enhanced NCI Database Browser.
- A total of 565 types of biological activities are predicted, covering areas like pharmacological effects, mechanisms of action, and toxicities.
- Users can perform complex searches using predicted activity probabilities combined with criteria such as physicochemical properties and structural fragments.