Scott D Bembenek | PubMed Health

PubMed2006

Calculation of the surface tension of oxygen using molecular-dynamics simulations.

The surface tension of oxygen at the liquid-vapor interface is calculated for the temperature range of 60-90 K using molecular-dynamics simulations and is shown to be within 1.0% error of experimental values for most of the temperatures studied. The potential used here is the same as in our previous study on liquid oxygen alone [S. D. Bembenek and B. M. Rice, J. Chem. Phys. 113, 2354 (2000)] and was optimized with an innovative statistical-mechanical method. The potential does not use a long-range cutoff nor a tail correction, which are usually considered necessary to obtain accurate values for the surface tension. We reason that the accuracy in surface tension is directly related to our parametrization method for the potential.

Journal Article↗

PubMed2005

Three-dimensional models of histamine H3 receptor antagonist complexes and their pharmacophore.

Molecular modeling was used to analyze the binding mode and activities of histamine H3 receptor antagonists. A model of the H3 receptor was constructed through homology modeling methods based on the crystal structure of bovine rhodopsin. Known H3 antagonists were interactively docked into the putative antagonist binding pocket and the resultant model was subjected to molecular mechanics energy minimization and molecular dynamics simulations which included a continuum model of the lipid bilayer and intra- and extracellular aqueous environments surrounding the transmembrane helices. The transmembrane helices stayed well embedded in the dielectric slab representing the lipid bilayer and the intra- and extracellular loops remain situated in the aqueous solvent region of the model during molecular dynamics simulations of up to 200 ps in duration. A pharmacophore model was calculated by mapping the features common to three active compounds three-dimensionally in space. The 3D pharmacophore model complements our atomistic receptor/ligand modeling. The H3 antagonist pharmacophore consists of two protonation sites (i.e. basic centers) connected by a central aromatic ring or hydrophobic region. These two basic sites can simultaneously interact with Asp 114 (3.32) in helix III and a Glu 206 (5.46) in helix V which are believed to be the key residues that histamine interacts with to stabilize the receptor in the active state. The interaction with Glu 206 is consistent with the enhanced activity resulting from the additional basic site. In addition to these two salt bridging interactions, the central region of these antagonists contains a lipophilic group, usually an aromatic ring, that is found to interact with several nearby hydrophobic side chains. The picture of antagonist binding provided by these models is consistent with earlier pharmacophore models for H3 antagonists with some exceptions.

Amino Acid Sequence↗

PubMed2004

A Web-based chemoinformatics system for drug discovery.

One of the key questions that must be addressed when implementing a chemoinformatics system is whether the tools will be designed for use by the expert user or by the "bench scientist." This decision can impact not only the style of tools that are rolled out, but is also a factor in terms of how these tools are delivered to the end users. The system that we outline here was designed for use by the non-expert user. As such, the tools that we discuss are in many cases simplified versions of some common algorithms used in chemoinformatics. In addition, the focus is on how to distribute these tools using a web-services interface, which greatly simplifies delivering new protocols to the end user.

Combinatorial Chemistry Techniques↗