Programming Libraries for Molecular Modeling
Shape TK is the basis for the ROCS application for shape-based similarity searching. The toolkit allows for fine control over optimization methods, molecule treatment and the nature of the query (grids, generic shapes). Shape TK facilitates the calculation of molecular descriptors for shape (steric multipoles), volume overlap between molecules, and spatial similarity of chemical groups (color force field), as well as the optimization of the latter two quantities.
Examples of use include aligning and comparing protein active sites, performing real-space fitting to electron density, shape fingerprinting , consensus shape generation, and discrimination between agonists and antagonists based on shared shapes .
Example of a result obtained from a combination of modeling toolkits:
conformers from Omega TK were overlain using Shape TK
while surfaces and coloring were generated by Spicoli TK.
- Small molecule shape-fingerprints Haigh, J. A., Pickup, B. T., Grant, J. A., Nicholls, A., J. Chem. Inf. Model., 2005, 45, 673.
- Scaffold hopping, synthesis and structure-activity relationships of 5,6-diaryl-pyrazine-2-amide derivatives: a novel series of CB1 receptor antagonists Boström, J., Berggren, K., Elebring, T., Greasley, P.J., Wilstermann, M., Bioorg Med Chem., 2007, 15, 4077.