Comprehensive two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC×GC/TOF-MS) has been applied to metabolomics analyses recently. However, retention time shifts in the two-dimensional gas chromatography will introduce difficulty to compare compound profiles obtained from multiple samples. In this work,…

Network-based systems biology tools including Pathway Studio 9.0 were used to identify Parkinson’s disease (PD) critical molecular players, drug targets, and underlying biological processes.  Utilizing several microarray gene expression datasets, biomolecular networks such as direct interaction, shortest path, and microRNA…

Basic chemometric methods for making empirical regression models for QSPR/QSAR are briefly described from a user's point of view. Emphasis is given to PLS regression, simple variable selection and a careful and cautious evaluation of the performance of PLS models…

Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology…

Fenestration morphology is a remarkable example of the synergy between structure and function. Through a better understanding of fenestration structure our understanding of its function will be enhanced. Fenestrations are transcellular pores that act as fundamental biological ultra-filters allowing diffusive…

BRCA1, a multi-domain protein, is mutated in a large percentage of hereditary breast and ovarian cancers.  BRCA1 is most often mutated in three domains or regions: the N-terminal RING domain, exons 11-13, and the BRCT domain.  The BRCA1 RING domain…

Proteins are the most multifaceted macromolecules in living systems and have various important functions, including structural, catalytic, sensory, and regulatory functions. Rational design of enzymes is a great challenge to our understanding of protein structure and physical chemistry and has…

A literature review concerning the unexpected species differences of the vertebrate innate immune response to lipid IVA was published in CSBJ prior to the present computational study to address the unpaired activity-sequence correlation of prototypic E. coli -type lipid A…

The albumin-binding domain is a small, three-helical protein domain found in various surface proteins expressed by gram-positive bacteria. Albumin binding is important in bacterial pathogenesis and several homologous domains have been identified. Such albumin-binding regions have been used for protein…

Molecular biological data has rapidly increased with the recent progress of the Omics fields, e.g., genomics, transcriptomics, proteomics and metabolomics that necessitates the development of databases and methods for efficient storage, retrieval, integration and analysis of massive data. The present…