Current Protein and Peptide Science - Volume 15, Issue 6, 2014

The advent of various advanced biological experimental techniques for discovery of conservations and interactions between molecules has prompted the study of biological regulation networks in a systematic way. The increasingly growth of organisms, genome-scale conservation and co-expression yield valuable data sources for exploring the functional and regulatory roles of biological systems. Graphs can be easily a Read More

With the development of structural genomics projects, the discrimination of native proteins from decoys has become one of the major challenges in protein structure prediction. In comparison with the energy function based techniques, amino acid network provides a simple but efficient method for the native structure selection. Amino acid network (AAN) is a graph representation of protein structure where amino acids in Read More

Accurate annotation of protein functions is still a big challenge for understanding life in the post-genomic era. Recently, some methods have been developed to solve the problem by incorporating functional similarity of GO terms into protein-protein interaction (PPI) network, which are based on the observation that a protein tends to share some common functions with proteins that interact with it in PPI network, and two similar Read More

Determination of binding sites between proteins is widely applied in many fields, such as drug design and the structural and functional analysis. The protein-protein binding sites can be formed by two subunits in a complex. Understanding energetics and mechanisms of complexes remains one of the essential problems in binding site prediction. We develop a system, P-Binder, for identifying binding sites based on shape compleme Read More

In order to transform protein sequences into the feature vectors, several works have been done, such as computing auto covariance (AC), conjoint triad (CT), local descriptor (LD), moran autocorrelation (MA), normalized moreaubroto autocorrelation (NMB) and so on. In this paper, we shall adopt these transformation methods to encode the proteins, respectively, where AC, CT, LD, MA and NMB are all represented by ‘+’ in a Read More

In silico pharmacology is a promising field in the current state-of drug discovery. This area exploits “proteinprotein Interaction (PPI) network analysis for drug discovery using the drug “target class”. To document the current status, we have discussed in this article how this an integrated system of PPI networks contribute to understand the disease pathways, present state-of-the-art drug target discovery and drug discover Read More

Castor bean (Ricinus communis L.) is an important oilseed crop for the rich hydroxylated triacylglycerol (TAG)-ricinoleate which is a raw material with wide applications in industry. Hydroxylated TAG synthesis occurs through complicated pathways among multiple subcellular organelles. Some crucial enzymes have been identified in previous studies. After analyzing the available castor tissue-specific transcriptome sequencing d Read More

Protein subcellular localization has been a long-standing key problem in investigating proteins’ function, which provides important clues for revealing their functions and aids in understanding their interactions with other biomolecules at the cellular level. Here, we systematically defined the organelle-focused proteomes and interactomes in Oryza sativa. A total of 83.42% of the whole rice proteome obtained their subcell Read More

MicroRNA(miRNA) is a small, single stranded non-coding RNA which plays an important regulatory role in gene expression. Additionally, miRNAs perform crucial functions in a wide range of biological processes. These functions may be exploited for miRNA-mediated regulation of protein-protein interaction and thus protein function. Many computational methods have been developed to predict the miRNA targets and to ex Read More

Selenium (Se) is an essential trace element for humans, plants and microorganisms. Inorganic selenium is present in nature in four oxidation states: selenate, selenite, elemental Se and selenide in decreasing order of redox status. These forms are converted by all biological systems into more bioavailable organic forms, mainly as the two seleno-amino acids selenocysteine and selenomethionine. Humans, plants and micr Read More

Arginine is widely used in such applications as protein refolding, solubilization of proteins and small molecules, protein and small molecule formulation, column chromatography and viral inactivation as summarized in this review. What makes arginine effective in these applications is largely based on its ability to suppress protein-protein interactions and protein-surface interactions. The mechanism of these widesprea Read More

Thioredoxin plays a crucial role in a wide number of physiological processes, which span from reduction of nucleotides to deoxyriboucleotides to the detoxification from xenobiotics, oxidants and radicals. The redox function of Thioredoxin is critically dependent on the enzyme Thioredoxin NADPH Reductase (TrxR). In view of its indirect involvement in the above mentioned physio/pathological processes, inhibition of TrxR is a Read More