Letters in Organic Chemistry - Volume 16, Issue 4, 2019

Protein phosphorylation is one of the most important post-translational modifications of proteins. Almost all processes that regulate the life activities of an organism as well as almost all physiological and pathological processes are involved in protein phosphorylation. In this paper, we summarize specific implementation and application of the methods used in protein phosphorylation site prediction such as the support v Read More

Malaria has been one of the serious infectious diseases caused by Plasmodium falciparum (P. falciparum). Mitochondrial proteins of P. falciparum are regarded as effective drug targets against malaria. Thus, it is necessary to accurately identify mitochondrial proteins of malaria parasite. Many algorithms have been proposed for the prediction of mitochondrial proteins of malaria parasite and yielded the better results. However, Read More

Protein-protein interactions play an important role in biological and cellular processes. Biochemistry experiment is the most reliable approach identifying protein-protein interactions, but it is time-consuming and expensive. It is one of the important reasons why there is only a little fraction of complete protein-protein interactions networks available by far. Hence, accurate computational methods are in a great need to predi Read More

In vivo, one of the most efficient biological mechanisms for expanding the genetic code and regulating cellular physiology is protein post-translational modification (PTM). Because PTM can provide very useful information for both basic research and drug development, identification of PTM sites in proteins has become a very important topic in bioinformatics. Lysine residue in protein can be subjected to many types of P Read More

S-nitrosylation is one of the most prominent posttranslational modification among proteins. It involves the addition of nitrogen oxide group to cysteine thiols forming S-nitrosocysteine. Evidence suggests that S-nitrosylation plays a foremost role in numerous human diseases and disorders. The incorporation of techniques for robust identification of S-nitrosylated proteins is highly anticipated in biological research and drug di Read More

Antifreeze proteins (AFPs) perform distinguishable roles in maintaining homeostatic conditions of living organisms and protect their cell and body from freezing in extremely cold conditions. Owing to high diversity in protein sequences and structures, the discrimination of AFPs from non- AFPs through experimental approaches is expensive and lengthy. It is, therefore, vastly desirable to propose a computational intelligent and hi Read More

The occurrence of epidemic avian influenza (EAI) not only hinders the development of a country's agricultural economy, but also seriously affects human beings’ life. Recently, the information collected from Google Trends has been increasingly used to predict various epidemics. In this study, using the relevant keywords in Google Trends as well as the multiple linear regression approach, a model was developed to predict the o Read More

In this work, support vector regression (SVR), an effective machine learning method, proposed by Vapnik was applied to establish QSAR model for a series of AchEI. Fourteen descriptors were selected for constructing the SVR mode by using mRMR-Forward feature selection method. The parameters (, C) were adjusted by leave-one-out cross validation (LOOCV) method which was used to judge the predictive power of diffe Read More

Protein structural class prediction is beneficial to protein structure and function analysis. Exploring good feature representation is a key step for this prediction task. Prior works have demonstrated the effectiveness of the secondary structure based feature extraction methods especially for lowsimilarity protein sequences. However, the prediction accuracies still remain limited. To explore the potential of secondary structure i Read More

The catalytic activity of the enzyme is different from that of the inorganic catalyst. In a high-temperature, over-acid or over-alkaline environment, the structure of the enzyme is destroyed and then loses its activity. Although the biochemistry experiments can measure the optimal PH environment of the enzyme, these methods are inefficient and costly. In order to solve these problems, computational model could be e Read More

Phages are widely distributed in locations populated by bacterial hosts. Phage proteins can be divided into two main categories, that is, virion and non-virion proteins with different functions. In practice, people mainly use phage virion proteins to clarify the lysis mechanism of bacterial cells and develop new antibacterial drugs. Accurate identification of phage virion proteins is therefore essential to understanding the phage lysis Read More

Colorectal cancer (CRC) is a common malignant tumor of the digestive tract occurring in the colon, which mainly divided into adenocarcinoma, mucinous adenocarcinoma, and undifferentiated carcinoma. However, autophagy is related to the occurrence and development of various kinds of human diseases such as cancer. There is little research on the relationship between CRC and autophagy. Hence, we performed multidim Read More

As an important post-transcriptional modification, adenosine-to-inosine RNA editing generally occurs in both coding and noncoding RNA transcripts in which adenosines are converted to inosines. Accordingly, the diversification of the transcriptome can be resulted in by this modification. It is significant to accurately identify adenosine-to-inosine editing sites for further understanding their biological functions. Currently, the ade Read More