Chou's 5-steps Rule Research Articles

The Graphical Studies of the Major Molecular Interactions for Neural Cell Adhesion Molecule (NCAM) Polysialylation by Incorporating Wenxiang Diagram into NMR Spectroscopy

Polysialylation is a process of polysialic acid (polySia) addition to neural cell adhesion molecule (NCAM), which is associated with tumor cell migration and progression in many metastatic cancers and neurocognition. Polysialylation can be catalyzed by two highly homologous mammalian polysialyltransferases (polySTs), ST8Sia II (STX) and ST8Sia IV (PST). It has been proposed that two polybasic domains, polybasic region (PBR) and polysialyltransferase domain (PSTD) in polySTs, are possible binding sites for the intermolecular interactions of polyST-NCAM and polyST-polySia, respectively, as well as the intramolecular interaction of PSTD-PBR. In this study, Chou's wenxiang diagrams of the PSTD and PBR are used to determine the key amino acids of these intermolecular and intramolecular interactions, and thus it may be helpful for the identification of the crucial amino acids in the polyST and for the understanding of the molecular mechanism of NCAM polysialylation by incorporating the wenxiang diagram and molecular modeling into NMR spectroscopy.

Prediction of Allergen and Non-Allergen Proteins Sequence via Chou's 5-Step Rule

Some specific kinds of proteins are responsible for the risk of immediate type I allergic reaction. Therefore, the proteins that are made to use in the consumer product should be checked for their allergic reactions before introducing them in the market. The FAO/WHO instructions for the assessment of allergic proteins depend on the linear sequence window identity and short peptide hits misclassify many proteins as allergen proteins. This study introduces the AllerPredictor model that predicts the allergen & non-allergen proteins depending on the sequence of proteins. Data was downloaded from two major databases, FARRP and UniProtKB. The results of this model were validated with the help of self-consistency testing, independence testing, and jackknife testing. The accuracy for self-consistency validation is 99.89%, for the independence testing is 74.23%, and for 10-fold cross-validation, it is 97.17%. To predict the allergen and non-allergen proteins, this AllerPredictor model has a better accuracy than other existing methods.

IPhosH-PseAAC: Identify Phosphohistidine Sites in Proteins by Blending Statistical Moments and Position Relative Features According to the Chou's 5-Step Rule and General Pseudo Amino Acid Composition.

Protein phosphorylation is one of the key mechanism in prokaryotes and eukaryotes and is responsible for various biological functions such as protein degradation, intracellular localization, the multitude of cellular processes, molecular association, cytoskeletal dynamics, and enzymatic inhibition/activation. Phosphohistidine (PhosH) has a key role in a number of biological processes, including central metabolism to signalling in eukaryotes and bacteria. Thus, identification of phosphohistidine sites in a protein sequence is crucial, and experimental identification can be expensive, time-taking, and laborious. To address this problem, here, we propose a novel computational model namely iPhosH-PseAAC for prediction of phosphohistidine sites in a given protein sequence using pseudo amino acid composition (PseAAC), statistical moments, and position relative features. The results of the proposed predictor are validated through self-consistency testing, 10-fold cross-validation, and jackknife testing. The self-consistency validation gave the 100 percent accuracy, whereas, for cross-validation, the accuracy achieved is 94.26 percent. Moreover, jackknife testing gave 97.07 percent accuracy for the proposed model. Thus, the proposed model iPhosH-PseAAC for prediction of iPhosH site has the great ability to predict the PhosH sites in given proteins.

The Remarkable Impacts of Gordon Life Science Institute

In this review paper, the remarkable impacts of the first Internet Institute, the Gordon Life Science Institute, as well as its profound and far-reaching influence have been systematically and comprehensively presented.

The Significant and Profound Impacts of Gordon Life Science Institute

In this short review paper, the significant and profound impacts of the Gordon Life Science Institute have been briefly presented with crystal clear convincingness.

The Significant and Profound Impacts of Gordon Life Science Institute

The “Gordon Life Science” or “GLS” Institute is the first Internet Institute in the world. Established by Prof. Dr. Kuo-Chen Chou in 2003, right after he was retired from “Pfizer Global Research and Development” in San Diego, California. There is a very interesting story for the name of Institute as elaborated below. After the “gangs of four” (including Mao Zedong's wife) was smashed and the complete failure of Mao “Cultural Revolution”, China was under the leadership of Deng Xiaoping, who took the policy of “韬光养晦”starting to open China’s door, the founder was invited by Professor Sture Forsén, the then “Chairman of Nobel Prize Committee”, to work in Chemical Center of Lund University as a Visiting Professor. It was very difficult for Swedish people to pronounce “Kuo-Chen Chou”. In order for his colleagues and friends there easier to pronounce his name, Professor Chou used “Gordon” as his name in Sweden. In 2003, about a quarter of century later, the same name was used for the Institute, meaning that Deng’s “韬光养晦” policy can stimulate a lot of great creativities.

The Significant and Profound Impacts of Gordon Life Science Institute

The Significant and Profound Impacts of Gordon Life Science Institute

The Significant and Profound Impacts of Gordon Life Science Institute

The Significant and Profound Impacts of Gordon Life Science Institute

Use Chou's 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information.

The knowledge of DNA-binding proteins would help to understand the functions of proteins better in cellular biological processes. Research on the prediction of DNA-binding proteins can promote the research of drug proteins and computer acidified drugs. In recent years, methods based on machine learning are usually used to predict proteins. Although great predicted performance can be achieved via current methods, researchers still need to invest more research in terms of the improvement of predicted performance. In this study, the prediction of DNA-binding proteins is studied from the perspective of evolutionary information and the support vector machine method. One machine learning model for predicting DNA-binding proteins based on evolutionary features by using Chou's 5-step rule is put forward. The results show that great predicted performance is obtained on benchmark dataset PDB1075 and independent dataset PDB186, achieving the accuracy of 86.05% and 75.30%, respectively. Thus, the method proposed is comparable to a certain degree, and it may work even better than other methods to some extent.

Use Chou's 5-Steps Rule With Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model.

Living organisms receive necessary energy substances directly from cellular respiration. The completion of electron storage and transportation requires the process of cellular respiration with the aid of electron transport chains. Therefore, the work of deciphering electron transport proteins is inevitably needed. The identification of these proteins with high performance has a prompt dependence on the choice of methods for feature extraction and machine learning algorithm. In this study, protein sequences served as natural language sentences comprising words. The nominated word embedding-based feature sets, hinged on the word embedding modulation and protein motif frequencies, were useful for feature choosing. Five word embedding types and a variety of conjoint features were examined for such feature selection. The support vector machine algorithm consequentially was employed to perform classification. The performance statistics within the 5-fold cross-validation including average accuracy, specificity, sensitivity, as well as MCC rates surpass 0.95. Such metrics in the independent test are 96.82, 97.16, 95.76 percent, and 0.9, respectively. Compared to state-of-the-art predictors, the proposed method can generate more preferable performance above all metrics indicating the effectiveness of the proposed method in determining electron transport proteins. Furthermore, this study reveals insights about the applicability of various word embeddings for understanding surveyed sequences.

Using the Chou's 5-steps rule, transient overexpression technique, subcellular location, and bioinformatic analysis to verify the function of Vitis vinifera O-methyltranferase 3 (VvOMT3) protein

3-Isobutyl-2-methoxypyrazine (IBMP) is an important odor compound that revives unripe grapes or poor-quality wine. The biosynthesis of IBMP in grape berries is under the catalysis of Vitis vinifera O-methyltranferase 3 (VvOMT3). The homologous verification in this paper was carried out with the transient overexpression technique. The results showed that both the expression levels of the VvOMT3 gene and the IBMP concentration in ‘Red globe’ grapes increased significantly, which suggested that VvOMT3 could function in the biosynthesis of IBMP. Based on β-glucuronidase (GUS) staining results, blue color was only observed in grape pulp, not in grape skin, which indicated that VvOMT3 was expressed in grape pulp. The outcomes of the subcellular location examination performed on the protoplasts of Arabidopsis thaliana showed that the VvOMT3 protein was located on the inner surface of the cytoplasmic membrane. In summary, the VvOMT3 enzyme may function at the inner surface of the cytoplasmic membrane of pulp cells during grape development. These results will provide a background for future research on the catalytic mechanisms of VvOMT3.

Gordon Life Science Institute and Its Impacts on Computational Biology and Drug Development

Gordon Life Science Institute is the first Internet Research Institute ever established in the world. It is a non-profit institute. Those scientists who really dedicate themselves to science and loving science more than anything else can become its member. In the friendly door-opened Institute, they can maximize their time and energy to engage in their scientific creativity. They have also believed that science would be more truthful and wonderful if scientists do not have to spend a lot of time on funding application, and that great scientific findings and creations in history were often made by those who were least supported or funded but driven by interesting imagination and curiosity. Recollected in this review article is its establishing and developing processes, as well as its philosophy and accomplishments. Particularly, its productive and by-productive outcomes have covered the following five very hot topics in bioinformatics and drug development: 1) PseAAC and PseKNC; 2) Disported key theory; 3) Wenxiang diagram; 4) Multi-label system prediction; 5) 5-steps rule. Their impacts on the proteomics and genomics as well as drug development are substantially and awesome.

The Development of Gordon Life Science Institute: Its Driving Force and Accomplishments

Established in 2004, Gordon Life Science Institute is the first Internet Research Institute in the world. It is a non-profit institute, a gift to science. Those scientists, who are really loving science more than anything else and have shown fantastic creativity in science, can become the membership of such Institute. Their driving force is not funding but firmly belief that scientists will do much better science if they do not have to spend a lot of time for funding application, and that great scientific findings in history were often discovered by those who were without funding at all but driven by profound imagination and curiosity. Summarized in this review are also the accomplishments of the Gordon Life Science Institute and its future perspective.

Coronavirus and Gordon Life Science Institute

The impacts of coronavirus to our planet are unprecedented; i.e., they are going to eliminate the entire mankind. Driven by such horrible situation, some philosophical viewpoints have naturally happened. Whether the “World End” must come? If yes, when? During this waiting period, the best way to do science is via the Internet Institute, such as “Gordon Life Science Institute”, and the results thus achieved will be most rewarding.

The Significant and Profound Impacts of Chou’s “wenxiang” Diagram

In this short review paper, the significant and profound impacts of the Chou’s “wenxiang diagram” have been briefly presented with crystal clear convincingness.

The Cradle of Gordon Life Science Institute and Its Development and Driving Force

Gordon Life Science Institute is the first Internet Research Institute ever established in the world. It is a non-profit institute. Those scientists who are really dedicated themselves to science and loving science more than anything else can become its member. In the friendly door-opened Institute, they can maximize their time and energy to engage in their scientific creativity. They have also believed that science would be more truthful and wonderful if scientists do not have to spend a lot of time on funding application, and that great scientific findings and creations in history were often made by those who were least supported or funded but driven by interesting imagination and curiosity. Recollected in this minireview is its establishing and developing processes, as well as its philosophy and accomplishments.

IQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou's 5-Steps Rule and Informative Physicochemical Properties.

Understanding of quorum-sensing peptides (QSPs) in their functional mechanism plays an essential role in finding new opportunities to combat bacterial infections by designing drugs. With the avalanche of the newly available peptide sequences in the post-genomic age, it is highly desirable to develop a computational model for efficient, rapid and high-throughput QSP identification purely based on the peptide sequence information alone. Although, few methods have been developed for predicting QSPs, their prediction accuracy and interpretability still requires further improvements. Thus, in this work, we proposed an accurate sequence-based predictor (called iQSP) and a set of interpretable rules (called IR-QSP) for predicting and analyzing QSPs. In iQSP, we utilized a powerful support vector machine (SVM) cooperating with 18 informative features from physicochemical properties (PCPs). Rigorous independent validation test showed that iQSP achieved maximum accuracy and MCC of 93.00% and 0.86, respectively. Furthermore, a set of interpretable rules IR-QSP was extracted by using random forest model and the 18 informative PCPs. Finally, for the convenience of experimental scientists, the iQSP web server was established and made freely available online. It is anticipated that iQSP will become a useful tool or at least as a complementary existing method for predicting and analyzing QSPs.

The Cradle of Gordon Life Science Institute and its Development and Driving Force

The Gordon Life Science Institute was established in 2003 at San Diego of California, USA. Its founder is Professor Dr. Kuo-Chen Chou. Its mission is to develop and apply new mathematical tools and physical concepts for understanding biological phenomena...

A Study for Therapeutic Treatment against Parkinson's Disease via Chou's 5-steps Rule.

The enzyme L-DOPA decarboxylase (DDC), also called aromatic-L-amino-acid decarboxylase, catalyzes the biosynthesis of dopamine, serotonin, and trace amines. Its deficiency or perturbations in expression result in severe motor dysfunction or a range of neurodegenerative and psychiatric disorders. A DDC substrate, L-DOPA, combined with an inhibitor of the enzyme is still the most effective treatment for symptoms of Parkinson's disease. In this review, we provide an update regarding the structures, functions, and inhibitors of DDC, particularly with regards to the treatment of Parkinson's disease. This information will provide insight into the pharmacological treatment of Parkinson's disease.

An insightful recollection since the birth of Gordon Life Science Institute about 17 years ago

An insightful recollection since the birth of Gordon Life Science Institute about 17 years ago