Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be m...

Bioinformatics is yielding extensive, and in some cases complete, genetic and biochemical information about individual cell types and cellular processes, providing the composition of living cells and the molecular structure of its components. These components together perform integrated cellular functions that now need to be analyzed. In particular, the functional definition of biochemical path...

RNA molecules with internal 20,50-branches are intermediates in RNA splicing, and branched RNAs have recently been proposed as retrotransposition intermediates. A broadly applicable in vitro synthetic route to branched RNA that does not require selfsplicing introns or spliceosomes would substantially improve our ability to study biochemical processes that involve branched RNA. We recently descr...

Non-diphtheriae Corynebacterium species have been increasingly recognized as the causative agents of infections in humans. Differential identification of these bacteria in the clinical microbiology laboratory by the most commonly used biochemical tests is challenging, and normally requires additional molecular methods. Herein, we present the annotated draft genome sequences of two isolates of "...

We present a simple method for determining the exact noise power spectra and related statistical properties for linear chemical reaction networks. The method is applied to reaction networks which are representative of biochemical processes such as gene expression. We find, for example, that a post-translational modification reaction can reduce the noise associated with gene expression. Our resu...

In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of intera...

Modeling of biochemical phenomena is based on formal reaction kinetics. This requires the translation of the original reaction systems into sets of differential equations expressing the effects of the various reaction steps. The temporal behavior of the system is obtained by solving the differential equations. We present the main concepts on which the formal approach of these two problems is ba...

Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities poses many computational challenges when taking stochastic noise into account. This paper proposes a new efficient finite difference method for computing parameter sensitivities of biochemical reactions. We employ propens...

RNA molecules with internal 2',5'-branches are intermediates in RNA splicing, and branched RNAs have recently been proposed as retrotransposition intermediates. A broadly applicable in vitro synthetic route to branched RNA that does not require self-splicing introns or spliceosomes would substantially improve our ability to study biochemical processes that involve branched RNA. We recently desc...