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A shape-based Gaussian docking function is constructed which uses Gaussian functions to represent the shapes of individual atoms. A set of 20 trypsin ligand-protein complexes are drawn from the Protein Data Bank (PDB), the ligands are separated from the proteins, and then are docked back into the active sites using numerical optimization of this function.(More)
The eight contributions here provide ample evidence that shape as a volume or as a surface is a vibrant and useful concept when applied to drug discovery. It provides a reliable scaffold for "decoration" with chemical intuition (or bias) for virtual screening and lead optimization but also has its unadorned uses, as in library design, ligand fitting, pose(More)
We apply a recently published method of text-based molecular similarity searching (LINGO) to standard data sets for the purpose of quantifying the accuracy of the approach. Our implementation is based on a pattern-matching finite state machine (FSM) which results in fast search times. The accuracy of LINGO is demonstrated to be comparable to that of a(More)
The optimal overlap between two molecular structures is a useful measure of shape similarity. However, it usually requires significant computation. This work describes the design of shape-fingerprints: binary bit strings that encode molecular shape. Standard measures of similarity between two shape-fingerprints are shown to be an excellent surrogate for(More)
We propose a molecule's chemistry can be hidden by representations of its shape and electrostatic field while retaining crucial, pharmaceutically relevant, information. Necessary, but not sufficient, to this proposition are the importance of shape and electrostatics to activity, the facility to easily represent, store and compare field properties, and(More)
An account is given of our contributions to the SAMPL2 challenge for vacuum-water transfer energies. These contributions include different charge sets and radii used with Poisson-Boltzmann continuum theory applied to a single low-energy conformation. A rationale for this approach is given, including a summary of what we have learnt over previous SAMPL(More)
This article examines the external and internal dimensions of post-conflict reconstruction in Sierra Leone. The United Nations, bilateral donors such as the United Kingdom, and transnational non-governmental organizations and aid agencies have been instrumental in providing much-needed external assistance to Sierra Leone during the latter stages of its(More)
Recently, the vacuum-phase molecular polarizability tensor of various molecules has been accurately modeled (Truchon et al., J Chem Theory Comput 2008, 4, 1480) with an intramolecular continuum dielectric model. This preliminary study showed that electronic polarization can be accurately modeled when combined with appropriate dielectric constants and atomic(More)