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.

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 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.

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 Implication of “I Am the Alpha and the Omega” to Internet Institutes

It is extremely fearful for the pestilences covering our Earth. Does that mean the “World End” is around the corner? For the so-called “Atheists” originally proposed by Karl Max and Friedrich Engels, “there is a Beginning, there must be an End”, meaning our Earth will finally no longer exist in the entire Universe by colliding with the other planet. According to Holly Bible, however, Jesus, will send out his angels to separate the wicked from the righteous and throw the former into the fiery furnace. For such a special time-period, many useful ideas or outcomes can be acquired by the Internet Institutes.

Noah’s Ark and Internet Institutes: When and Why?

The damage of coronavirus to our Earth is unprecedented that is going to kill the entire human beings. Facing this kind of situation, there are two completely different kinds of viewpoints. According to the philosophy of “Atheists” Karl Max and Friedrich Engels, “there is a Bigging, there must be an End”, meaning our Earth will eventually collide with the other planet and be destroyed completely. According to Holly Bible, however, Jesus, will come down again to bring Godly people to the Heaven and leave the remaining in the coronavirus-hell. During this waiting period, the “Internet Institutes” can provide the most useful knowledge for the other planets.

The Most Important Ethical Concerns in Science

The most unethical behaviors in science are of falsifying data and stealing ideas from previous investigators. But for publishing papers with high similarity and editing papers with coercion, it is necessary to carry out a concrete analysis case by case.

Pse-in-One 2.0: An Improved Package of Web Servers for Generating Various Modes of Pseudo Components of DNA, RNA, and Protein Sequences

Pse-in-One 2.0 is a package of web-servers evolved from Pse-in-One (Liu, B., Liu, F., Wang, X., Chen, J. Fang, L. & Chou, K.C. Nucleic Acids Research, 2015, 43:W65-W71). In order to make it more flexible and comprehensive as suggested by many users, the updated package has incorporated 23 new pseudo component modes as well as a series of new feature analysis approaches. It is available at http://bioinformatics.hitsz.edu.cn/Pse-in-One2.0/. Moreover, to maximize the convenience of users, provided is also the stand-alone version called “Pse-in-One-Analysis”, by which users can significantly speed up the analysis of massive sequences.

Prediction of protein folding rates from primary sequence by fusing multiple sequential features

We have developed a web-server for predicting the folding rate of a protein based on its amino acid sequence information alone. The web- server is called Pred-PFR (Predicting Protein Folding Rate). Pred-PFR is featured by fusing multiple individual predictors, each of which is established based on one special feature derived from the protein sequence. The ensemble pre-dictor thus formed is superior to the individual ones, as demonstrated by achieving higher correlation coefficient and lower root mean square deviation between the predicted and observed results when examined by the jack-knife cross-validation on a benchmark dataset constructed recently. As a user-friendly web- server, Pred-PFR is freely accessible to the public at www.csbio.sjtu.edu.cn/bioinf/Folding Rate/.

pLoc_Deep-mVirus: A CNN Model for Predicting Subcellular Localization of Virus Proteins by Deep Learning

The recent worldwide spreading of pneumonia-causing virus, such as Coronavirus, COVID-19, and H1N1, has been endangering the life of human beings all around the world. In order to really understand the biological process within a cell level and provide useful clues to develop antiviral drugs, information of virus protein subcellular localization is vitally important. In view of this, a CNN based virus protein subcellular localization predictor called “pLoc_Deep-mVirus” was developed. The predictor is particularly useful in dealing with the multi-sites systems in which some proteins may simultaneously occur in two or more different organelles that are the current focus of pharmaceutical industry. The global absolute true rate achieved by the new predictor is over 97% and its local accuracy is over 98%. Both are transcending other existing state-of-the-art predictors significantly. It has not escaped our notice that the deep-learning treatment can be used to deal with many other biological systems as well. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new predictor has been established at http://www.jci-bioinfo.cn/pLoc_Deep-mVirus/.

pLoc_Deep-mHum: Predict Subcellular Localization of Human Proteins by Deep Learning

Recently, the life of human beings around the entire world has been endangering by the spreading of pneumonia-causing virus, such as Coronavirus, COVID-19, and H1N1. To develop effective drugs against Coronavirus, knowledge of protein subcellular localization is indispensable. In 2019, a predictor called “pLoc_bal-mHum” was developed for identifying the subcellular localization of human proteins. Its predicted results are significantly better than its counterparts, particularly for those proteins that may simultaneously occur or move between two or more subcellular location sites. However, more efforts are definitely needed to further improve its power since pLoc_bal-mHum was still not trained by a “deep learning”, a very powerful technique developed recently. The present study was devoted to incorporate the “deep-learning” technique and develop a new predictor called “pLoc_Deep-mHum”. The global absolute true rate achieved by the new predictor is over 81% and its local accuracy is over 90%. Both are overwhelmingly superior to its counterparts. Moreover, a user-friendly web-server for the new predictor has been well established at http://www.jci-bioinfo.cn/pLoc_Deep-mHum/, which will become a very useful tool for fighting pandemic coronavirus and save the mankind of this planet.

pLoc_Deep-mEuk: Predict Subcellular Localization of Eukaryotic Proteins by Deep Learning

Recently, the life of worldwide human beings has been endangering by the spreading of pneu- monia-causing virus, such as Coronavirus, COVID-19, and H1N1. To develop effective drugs against Coronavirus, knowledge of protein subcellular localization is prerequisite. In 2019, a predictor called “pLoc_bal-mEuk” was developed for identifying the subcellular localization of eukaryotic proteins. Its predicted results are significantly better than its counterparts, particularly for those proteins that may simultaneously occur or move between two or more subcellular location sites. However, more efforts are definitely needed to further improve its power since pLoc_bal-mEuk was still not trained by a “deep learning”, a very powerful technique developed recently. The present study was devoted to incorporating the “deep- learning” technique and developed a new predictor called “pLoc_Deep-mEuk”. The global absolute true rate achieved by the new predictor is over 81% and its local accuracy is over 90%. Both are overwhelmingly superior to its counterparts. Moreover, a user-friendly web- server for the new predictor has been well established at http://www.jci-bioinfo.cn/pLoc_Deep-mEuk/, by which the majority of experimental scientists can easily get their desired data.

pLoc-mGpos: Incorporate Key Gene Ontology Information into General PseAAC for Predicting Subcellular Localization of Gram-Positive Bacterial Proteins

The basic unit in life is cell.?It contains many protein molecules located at its different organelles. The growth and reproduction of a cell as well as most of its other biological functions are performed via these proteins. But proteins in different organelles or subcellular locations have different functions. Facing?the avalanche of protein sequences generated in the postgenomic age, we are challenged to develop high throughput tools for identifying the subcellular localization of proteins based on their sequence information alone. Although considerable efforts have been made in this regard, the problem is far apart from being solved yet. Most existing methods can be used to deal with single-location proteins only. Actually, proteins with multi-locations may have some special biological functions that are particularly important for drug targets. Using the ML-GKR (Multi-Label Gaussian Kernel Regression) method,?we developed a new predictor called “pLoc-mGpos” by in-depth extracting the key information from GO (Gene Ontology) into the Chou’s general PseAAC (Pseudo Amino Acid Composition)?for predicting the subcellular localization of Gram-positive bacterial proteins with both single and multiple location sites. Rigorous cross-validation on a same stringent benchmark dataset indicated that the proposed pLoc-mGpos predictor is remarkably superior to “iLoc-Gpos”, the state-of-the-art predictor for the same purpose.?To maximize the convenience of most experimental scientists, a user-friendly web-server for the new powerful predictor has been established at http://www.jci-bioinfo.cn/pLoc-mGpos/, by which users can easily get their desired results without the need to go through the complicated mathematics involved.

Showcase to Illustrate How the Web-Server pLoc_Deep-mHum Is Working

Recently, a very useful method called “pLoc_Deep-mHum” has been proposed for finding against the Pandemic COVID-19. Illustrated in this short report is a step-by-step guide for how to use its web-server.

Lead induced overactivation of phagocytes and variation in enzymatic and non-enzymatic antioxidant defenses in intestinal macrophages of <i>Channa punctatus</i>

The aim of this study is to assess the adverse effects of lead, a well-documented non-essential element that occurs naturally in the environment, on Channa punctatus, in relation with ROS production and oxidative stress. Fishes were sampled, acclimatized and kept treated or untreated with lead (9.43 mg/L) under observation for 4 days. At day 4, respiratory burst activity, lipid peroxidation activity and superoxide dismutase level increased significantly in treated group as compared to the control. On the contrary, catalase, glutathione S-transferase, glutathione peroxidase, glutathione reductase and reduced glutathione activity decreased on treatment with lead. These results suggest that heavy metal like lead induces oxidative stress, influences the antioxidant defense system and may lead to physiological disorders rendering the health and survival of exposed fish to a compromised state.

Other Mountain Stones Can Attack Jade: The 5-Steps Rule

Since the 5-steps rule was proposed in 2011, it has been widely used in many areas of molecular biology, both theoretical and experimental. It can be even used to deal with the commercial problems and bank systems, as well as material science systems. Just like the machine-learning algorithms, it is the jade for nearly all the statistical systems.

The Problem of Elsevier Series Journals Online Submission by Using Artificial Intelligence

With the rapid development of artificial intelligence [AI], many journals including Elsevier series, Springer series, John Willey and Son series, American Chemical Society (ACS) series, and Bentham Science (BMS) series, have used AI technique to run the online submission for authors. Among the aforementioned five series journals, the Elsevier and BMS have some critical shortcomings that have discouraged many authors.

Proposing 5-Steps Rule Is a Notable Milestone for Studying Molecular Biology

In this current minireview, the cradle of the “5-steps rule” or “5-step rules”, along with its essence and advances, has been recalled. Born in 2011, its impacts on molecular biology are both substantial and rapid, fully indicating the “5-steps rule” is no double a remarkable and profound milestone in molecular biology.

Using Similarity Software to Evaluate Scientific Paper Quality Is a Big Mistake

Using similarity software to examine the quality of scientific papers is a nuisance. The significance of a scientific paper should be decided by the acknowledged experts. The practice of using the computer program to decide scientific papers must be rescinded or voided.

The Chemical Mechanism of Pestilences or Coronavirus Disease 2019 (COVID-19)

In this paper, the chemical mechanism of the coronavirus disease 2019 (COVID-19) has been explored and clearly revealed.