openbabel Archive

  • Does size matter?

    Does size matter?

    The goal of drug discovery is to find potent and selective inhibitors for particular targets. A good ligand thus should be small (for better bio-availability) and potent. The larger is the inhibitor, the more there are ways to interact with specific features of a certain...

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  • How good are biological data – II: Trombine, GSK, GPCR

    How good are biological data – II: Trombine, GSK, GPCR

    Many bindign affinity prediction methods, such as scores and QSAR models, rely on availability of accurate information on binding constants. The figure on the left is a result of our sdf-file parser applied to trombine (blue) and GSK (yellow) binding data from BindingDB database. The...

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  • How good are biological experiments? HERG binding data analysis

    How good are biological experiments? HERG binding data analysis

    A correlation between predicted and expermentally measured values of biological activity is a natural measure of a model quality. For instance, QUANTUM docking software calculates binding free energies, which are directly comparable with experimental values of -p(binding constant, Kd). Root mean squared error between the...

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