MOTIVATION To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo. RESULTS By probabilistically modeling mutations in the viruses isolated from HIV-1 B subtype patients, we present a unique statistical procedure that would first identify V3 determinants associated with the usage of different co-receptors cooperatively or independently, and t...

With the recent discovery of the ubiquity of organic material in tropospheric aerosols, it has been postulated that the rates of water evaporation and condensation into the aerosols could be affected by thin surfactant films, which could ultimately affect cloud formation. Nathanson et al. have begun to study the effect of water evaporation from sulfuric acid solutions through the short-chain su...

Virtual screening, or in silico screening, is a new approach attracting increasing levels of interest in the pharmaceutical industry as a productive and cost-effective technology in the search for novel lead compounds. Although the principles involved—the computational analysis of chemical databases to identify compounds appropriate for a given biological receptor—have been pursued for several ...

In addition, they do not need to be poled because they directly crystallize from melt or solution into the ferroelectric (β-) phase. Piezoelectricity in these materials is related to the electronegativity difference in hydrogen and fl uorine atoms, which determines an effective dipole moment in the direction normal to the carbon backbone. Consequently, these fi lms or nanostructures are often u...

Computer-based molecular modeling of single stranded polysaccharide chains is capable of a quantitative description of the polymer chain dimensions in dilute aqueous solution. The influence of glycosidic linkage position and stereochemistry on the local chain trajectory is now well understood. Some illustrative results of modeling of this sort are reported here. More recent efforts to understan...

The recent advances in genetic engineering, high powered computing and global optimization continue to stimulate interest in the area of molecular modeling and protein structure prediction. The goal of these eeorts is the ability to correctly predict native protein conformations and the binding interactions of macromolecules. These two problems currently dominate the eld of computational chemis...

In molecular shape analysis and in the analysis of various molecular functions used in modeling chemical reactions and biochemical interactions, it is often useful to generate transformations that interconvert various molecular models into one another. Some of these models are continua whereas some others have disconnected parts or even separated discrete points. The interconversion between suc...

Since most experimental observations are performed at constant temperature and pressure, the isothermal-isobaric (NPT ) ensemble has been widely used in molecular simulations. Nevertheless, the NPT ensemble has only recently been placed on a rigorous foundation. The proper formulation of the NPT ensemble requires a “shell” particle to uniquely identify the volume of the system, thereby avoiding...

Artificial receptors have been in use for several decades as sensor elements, in affinity separation, and as models for investigation of molecular recognition . Although there have been numerous publications on the use of molecular modeling in characterization of their affinity and selectivity, very few attempts have been made on the application of molecular modeling in computational design of ...