Current Bioinformatics - Volume 8, Issue 5, 2013

The identification of signal peptides and signal anchors is critical to understand the related biological mechanisms, and to find more effective vehicles for proteins production. Instead of studying signal peptides and signal anchors of single species separately, we developed a multi-tasking learning framework to investigate them across species simultaneously. By a multi-tasking feature selection method, we identified 12 imp Read More

Mainly based on pKa (NH3+) values of amino acid, a novel graphical method without degeneracy for protein sequences has been proposed firstly, which assists in viewing, aligning and comparing multiple sequences visually. Then, a new algorithm to extract a 40-dimensional numerical vector from graphical curves has been presented to characterize protein sequences. The similar relationship among sequences is computed by Read More

Protein complexes involve in most if not all of essential biological processes in a living cell. Many attempts have been devoted to identify protein complexes using computational methods, most of which exploit protein-protein interaction networks to search intensively interacting proteins as a protein complex. Besides identifying protein complexes, knowing their biological functions may help unlock their molecular mechanisms Read More

The PredictFold-PSS-3D1D is an online protein fold recognition web server used to predict the possible folds from the twilight zone protein sequences. In this server, an improved 3D1D profile method (Ganesan and Parthasarathy, J. Struct. Funct. Genomics, 12, 181-189, 2011) is employed, wherein, the inclusion of predicted secondary structure information improves fold recognition. The PredictFold-PSS-3D1D ser Read More

Identifying protein coding regions of DNA sequences is an important step in gene annotation. It is well-known that the protein coding regions of most genomic sequences exhibit a period-3 pattern due to non-uniform distribution of codons. In order to identify protein coding regions more efficiently, a new identification approach was proposed by combining chirp z transform and wavelet transform based on period-3 proper Read More

Knowledge of mechanism of small molecules in metabolic pathway is critical to design specific and effective inhibitors for metabolic pathway. As some small molecules are involved in more than one pathway, it is crucial to use an accurate and robust approach to correctly map the small molecule in specific metabolic pathway that it is involved in. In this article, small molecules are studied using the Minimal-Redundancy-M Read More

In this article, we determine an optimal set of enzymes which is needed to be expressed at a specific level, in order to maximize the production of the target metabolite, spermine, from the substrate, ornithine, in the polyamine metabolic pathway. The pathway thus obtained is compared with the optimal pathway obtained using the existing extreme pathway analysis method. The results are appropriately validated through liter Read More

Many people suffer from oral squamous cell carcinoma (OSCC), a kind of cancer with high severity and prevalence. The usual diagnostic method of oral squamous cell carcinoma is still very primitive by visually examining the mouth. When patients have a definitive diagnosis, they usually have missed the optimal therapeutic period. Therefore, it is essential to diagnose OSCC as early as possible. Microarray technology has been Read More

Adverse effects of HIV infection treatment cannot be ignored because the occurrences of undesired adverse effects will result in low drug adherence and influence the outcome of HIV treatment. Adverse effects are significantly associated with gender. However, the role of gender in the occurrences of adverse effects has not been clearly explored. In order to provide additional guidance to prescription, we analyzed th Read More

DNA replication is the basis for biological inheritance, involving a series of sophisticated biochemical processes. Over the past decades, numerous in vitro or in vivo experiments have been implemented among a variety of organisms. While these resource-intensive techniques may always be costly, time-consuming or unable to measure the replication process on a global scale. Recently, mathematical modeling and computati Read More

G-protein-coupled receptors (GPCRs) mediate diverse biological functions through intracellular signal cascades initiated by intracellular G-protein coupling following extracellular agonist binding. GPCRs are quintessential targets for drug design due to their involvement in pathophysiological conditions. The difficulty associated with GPCR crystallization and lack of accurate computational method for GPCR modeling constitutes Read More