Detecting remote homology proteins is a challenging problem for both basic research and drug development. Although there are a couple of methods to deal with this problem, the benchmark datasets based on which the exi...Detecting remote homology proteins is a challenging problem for both basic research and drug development. Although there are a couple of methods to deal with this problem, the benchmark datasets based on which the existing methods were trained and tested contain many high homologous samples as reflected by the fact that the cutoff threshold was set at 95%. In this study, we reconstructed the benchmark dataset by setting the threshold at 40%, meaning none of the proteins included in the benchmark dataset has more than 40% pairwise sequence identity with any other in the same subset. Using the new benchmark dataset, we proposed a new predictor called “dRHP-GreyFun” based on the grey modeling and functional domain approach. Rigorous cross-validations have indicated that the new predictor is superior to its counterparts in both enhancing success rates and reducing computational cost. The predictor can be downloaded from https://github.com/jcilwz/dRHP-GreyFun.展开更多
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...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.展开更多
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...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.展开更多
In this short review paper, the significant and profound impacts of the 5-steps rule have <span style="mso-bookmark:OLE_LINK2;"><span style="mso-bookmark:OLE_LINK1;"><span lang="...In this short review paper, the significant and profound impacts of the 5-steps rule have <span style="mso-bookmark:OLE_LINK2;"><span style="mso-bookmark:OLE_LINK1;"><span lang="EN-US" style="line-height: 97%;font-family:;" capt",serif;font-size:11pt;"="" pro="" minion="">been briefly recalled with crystal clear convincingness.</span></span></span>展开更多
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 anyt...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.展开更多
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 ...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.展开更多
The biological </span><span style="font-family:Verdana;font-size:12px;">principal</span><span style="font-family:Verdana;font-size:12px;"> or its detailed mechanism for the ...The biological </span><span style="font-family:Verdana;font-size:12px;">principal</span><span style="font-family:Verdana;font-size:12px;"> or its detailed mechanism for the pandemic coronavirus disease 2019 (COVID-19) has been investigated and analyzed from the topological entropy approach. The findings thus obtained have provided very useful clues and information for developing both powerful and safe vaccines against the pandemic COVID-19.展开更多
A systematic introduction has been presented for the recent advances in predicting protein subcellular localization in the multi-label systems, where the constituent proteins may simultaneously occur or move between t...A systematic introduction has been presented for the recent advances in predicting protein subcellular localization in the multi-label systems, where the constituent proteins may simultaneously occur or move between two or more location sites and hence have exceptional biological functions worthy of our special notice. All the predictors included in this review each have a user-friendly web-server, by which the majority of experimental scientists can very easily acquire their desired data without the need to go through the complicated mathematics involved.展开更多
Current coronavirus pandemic has endangered the entire mankind life. The reported cas-es are increasing exponentially. Information of protein post-translational modification (PTM) can provide useful clues to develop a...Current coronavirus pandemic has endangered the entire mankind life. The reported cas-es are increasing exponentially. Information of protein post-translational modification (PTM) can provide useful clues to develop antiviral drugs. According to our recent works, the PTM prediction can be significantly improved by widening the samples of training da-taset. Based on such an idea, a new predictor called “iSulf_Wide-PseAAC” has been de-veloped. Its accuracy is overwhelmingly higher than its counterparts. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new pre-dictor has been established at http://121.36.221.79/Isulf_Pse/, which will become a very useful tool for fighting pandemic coronavirus and save the mankind of this planet.展开更多
Phosphoaspartate is one of the major components of eukaryotes and prokaryotic two-component signaling pathways,and it communicates the signal from the sensor of histidine kinase,through the response regulator,to the D...Phosphoaspartate is one of the major components of eukaryotes and prokaryotic two-component signaling pathways,and it communicates the signal from the sensor of histidine kinase,through the response regulator,to the DNA alongside transcription features and initiates the transcription of correct response genes.Thus,the prediction of phosphoaspartate sites is critical,and its experimental identification can be expensive,time-consuming,and tedious.For this purpose,we propose iPhosD-PseAAC,a new computational model for predicting phosphoaspartate sites in a particular protein sequence using Chou’s 5-steps rues:(1)Benchmark dataset.(2)The feature extraction techniques such as pseudo amino acid composition(PseAAC),statistical moments,and position relative features.(3)For the classification,artificial neural network AAN will be used.(4)In this step,10-fold cross-validation and self-consistency testing will be used for validation.For self-consistency testing,100%Acc is achieved,whereas,for 10-fold crossvalidation 95.14%Acc,95.58%Sn,94.70%Sp and 0.95 MCC are observed.(5).The final step is the development of a user-friendly web server for the ease of users.Thus,the iPhosD-PseAAC is the first and novel predictor for accurate and efficient identification of phosphoaspartate sites.展开更多
文摘Detecting remote homology proteins is a challenging problem for both basic research and drug development. Although there are a couple of methods to deal with this problem, the benchmark datasets based on which the existing methods were trained and tested contain many high homologous samples as reflected by the fact that the cutoff threshold was set at 95%. In this study, we reconstructed the benchmark dataset by setting the threshold at 40%, meaning none of the proteins included in the benchmark dataset has more than 40% pairwise sequence identity with any other in the same subset. Using the new benchmark dataset, we proposed a new predictor called “dRHP-GreyFun” based on the grey modeling and functional domain approach. Rigorous cross-validations have indicated that the new predictor is superior to its counterparts in both enhancing success rates and reducing computational cost. The predictor can be downloaded from https://github.com/jcilwz/dRHP-GreyFun.
文摘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.
文摘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.
文摘In this short review paper, the significant and profound impacts of the 5-steps rule have <span style="mso-bookmark:OLE_LINK2;"><span style="mso-bookmark:OLE_LINK1;"><span lang="EN-US" style="line-height: 97%;font-family:;" capt",serif;font-size:11pt;"="" pro="" minion="">been briefly recalled with crystal clear convincingness.</span></span></span>
文摘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.
文摘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.
文摘The biological </span><span style="font-family:Verdana;font-size:12px;">principal</span><span style="font-family:Verdana;font-size:12px;"> or its detailed mechanism for the pandemic coronavirus disease 2019 (COVID-19) has been investigated and analyzed from the topological entropy approach. The findings thus obtained have provided very useful clues and information for developing both powerful and safe vaccines against the pandemic COVID-19.
文摘A systematic introduction has been presented for the recent advances in predicting protein subcellular localization in the multi-label systems, where the constituent proteins may simultaneously occur or move between two or more location sites and hence have exceptional biological functions worthy of our special notice. All the predictors included in this review each have a user-friendly web-server, by which the majority of experimental scientists can very easily acquire their desired data without the need to go through the complicated mathematics involved.
文摘Current coronavirus pandemic has endangered the entire mankind life. The reported cas-es are increasing exponentially. Information of protein post-translational modification (PTM) can provide useful clues to develop antiviral drugs. According to our recent works, the PTM prediction can be significantly improved by widening the samples of training da-taset. Based on such an idea, a new predictor called “iSulf_Wide-PseAAC” has been de-veloped. Its accuracy is overwhelmingly higher than its counterparts. To maximize the convenience for most experimental scientists, a user-friendly web-server for the new pre-dictor has been established at http://121.36.221.79/Isulf_Pse/, which will become a very useful tool for fighting pandemic coronavirus and save the mankind of this planet.
基金the Deanship of Scientific Research(DSR)at King Abdulaziz University,Jeddah,https://dsr.kau.edu.sa/Default-305-EN under Grant No.G:136-611-1441.
文摘Phosphoaspartate is one of the major components of eukaryotes and prokaryotic two-component signaling pathways,and it communicates the signal from the sensor of histidine kinase,through the response regulator,to the DNA alongside transcription features and initiates the transcription of correct response genes.Thus,the prediction of phosphoaspartate sites is critical,and its experimental identification can be expensive,time-consuming,and tedious.For this purpose,we propose iPhosD-PseAAC,a new computational model for predicting phosphoaspartate sites in a particular protein sequence using Chou’s 5-steps rues:(1)Benchmark dataset.(2)The feature extraction techniques such as pseudo amino acid composition(PseAAC),statistical moments,and position relative features.(3)For the classification,artificial neural network AAN will be used.(4)In this step,10-fold cross-validation and self-consistency testing will be used for validation.For self-consistency testing,100%Acc is achieved,whereas,for 10-fold crossvalidation 95.14%Acc,95.58%Sn,94.70%Sp and 0.95 MCC are observed.(5).The final step is the development of a user-friendly web server for the ease of users.Thus,the iPhosD-PseAAC is the first and novel predictor for accurate and efficient identification of phosphoaspartate sites.
