The displacement of solvent molecules from binding sites plays a critical role in the thermodynamics of biomolecular recognition and other complex interactions. For example, proteins and ligands experience changes in hydration as they interact, and understanding the affinities of ligands with protein active sites can be valuable in the design of molecules such as pharmaceutical candidates. Numerous computational approaches have been used to describe and predict the free energy of molecular interactions which involve the displacement or rearrangement of water, but previous approaches have involved simplifying assumption that risk limiting generality. An improved method is needed for modeling the thermodynamics of water in confined molecular spaces, with particular focus on its application to drug design by describing interactions between a ligand and its receptor. (more...)

Cell-based systems for in vitro biomarker profiling of drug efficacy or discovery. (more...)

UC Irvine biologists, chemists and computer scientists have identified an elusive pocket on the surface of the p53 protein that can be targeted by cancer-fighting drugs. The finding heralds a new treatment approach, as mutant forms of this protein are implicated in nearly 40 percent of diagnosed cases of cancer, which kills more than half a million Americans each year. (more...)

Researchers at the University of California, Berkeley have developed an invention that consists of an angular interferometer able to measure angle variations of a coherent, collimated light source with an accuracy below 30 nrad. The optical setup is compact and consists of a few simple optical components. The novelty of this innovation lies in the use of a simple, cost-effect technique to amplify the sensitivity of the instrument. The disclosed invention is in principle capable of being integrated into more compact, high-sensitivity commercial instruments for a fraction of the cost of current, state-of-the-art instruments (currently exceeding $30,000).   Commercial devices used to measure the angular deviation of a single beam include autocollimators and interferometers. The highest resolution offered by a commercial system is 25 nrad. The disclosed angular interferometer is able to measure relative angle variations (of a sample beam relative to a reference beam) below 30 nrad, though the resolution is known to currently be limited by the specific details of the current application and can therefore be further reduced with minor, inexpensive improvements. (more...)

Assemblies of next generation sequencing (NGS) data, while accurate, still contain a substantial number of errors that need to be corrected after the assembly process. Earlier assembly algorithms developed for Sanger sequencing follow an "overlap - layout - consensus" paradigm, where consensus refers to fixing errors in the contigs. Since this paradigm faces difficulties in short read assembly, most NGS assemblers employ a de Bruijn graph approach that effectively deals with large amounts of data. However, most NGS assemblers neglect the consensus step, i.e., there exists no postprocessing of the contigs in Velvet and many other popular assemblers. Relying on high and uniform coverage, NGS assembly algorithms push the burden of producing high quality assemblies onto the construction of the de Bruijn graph. Our work demonstrates that NGS assemblers can benefit from the use of a consensus step. There are currently no tools that aim to accomplish this same goal. (more...)

To understand the flow of genetic information at the systems level dictates that one must have fundamental knowledge of the organizational structure of the bacterial genome. These organizational elements include, but are not limited to, promoters, transcription start sites, open reading frames, regulatory noncoding regions, untranslated regions, and transcription units. Establishing the organizational structure of a genome is a challenging task that requires multiple simultaneous genome scale measurements in order to identify all gene products and how they interact with the genome (e.g., transcription factor binding to regulatory sequences). (more...)

UC San Diego inventors have invented a very general method to design and create new compounds with anti-bacterial, anti-fungal, anti-cancer, or other bioactive properties. Different from the existing art, where the biological effect of a compound must be determined, this invention allows for compounds to be designed and created with these effects known a priori. For example, this shortcoming, which the current invention overcomes, is part of the existing art being applied to anti-bacterial synthesis—such as mutational biosynthesis, genetic engineering, structure-based drug design, or interrogation of novel natural products.Slide Show Presentation (more...)

Researchers at the University of California, Irvine, have developed a method for the computational optimization of DNA sequences that encode their own correct self-assembly. (more...)

BACKGROUND: Genetic engineering of bacteria has become a prevalent way of producing chemicals, providing a cost-effective, scalable, and environmentally safe manufacturing process. However, maximizing the final product titer remains a challenge, requiring the optimization of the bacteria’s metabolism and the identification of the optimal protein production rates. Currently, the production rates of these proteins are determined through trial and error, by random mutagenesis, or equivalent random selection methods. As such, the development costs are typically very high.   TECHNOLOGY:   UCSF researchers have developed a novel methodology that allows the user to select the production rate of a given protein from very low to very high rates (1 to 100000), thus eliminating the use of trial and error techniques during the optimization process and enabling extremely high protein expression levels. The method is accessible via interactive web-based software. (more...)