The biological principal 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.
KeywordsVaccineCellularCoronavirusPandemic COVID-19Spatial and Time EntropyTopological EntropyChou’s 5-Steps Rule
Fang, L., Wang, X., Lai, Z., Zhang, D., Wu, M., Pan, Z., Wang, L., Tang, K., Qian, D., Huang, Z., Wang, X., Chen, H. and Chou, K.C. (2020) Reveal the Molecular Principle of Coronavirus Disease 2019 (COVID-19). Index of Sciences, 12, 1-13. https://doi.org/10.4236/ns.2020.1211063
Zhang, D., Fang, L., Wang, L., Pan, Z., Lai, Z., Wu, M., Tang, K., Ludan, L., Qian, D., Huang, Z., Wang, X., Chen, H. and Chou, K.C. (2020) The Physical Principle of Coronavirus Disease 2019 (COVID-19). Index of Sciences, 12, 1-13. https://doi.org/10.4236/ns.2020.1211063
Zhang, D., Fang, L., Wang, L., Pan, Z., Lai, Z., Wu, M., Tang, K., Ludan, L., Qian, D., Huang, Z., Wang, X., Chen, H. and Chou, K.C. (2020) The Chemical Mechanism of Pestilences or Coronavirus Disease 2019 (COVID-19). Natural Science, 12, 717-725. https://doi.org/10.4236/ns.2020.1211063
Butt, A.H. and Khan, Y.D. (2018) Prediction of S-Sulfenylation Sites Using Statistical Moments Based Features via Chou’s 5-Step Rule. International Journal of Peptide Research and Therapeutics (IJPRT), 17, 711-738.
Awais, M., Hussain, W., Khan, Y.D., Rasool, N., Khan, S.A. and Chou, K.C. (2019) 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. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 19, 1-21. https://doi.org/10.1109/TCBB.2019.2919025
Barukab, O., Khan, Y.D., Khan, S.A. and Chou, K.C. (2019) iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou’s 5-Steps Rule and Pseudo Components. Current Genomics, 20, 306-320. https://doi.org/10.2174/1389202920666190819091609
Butt, A.H. and Khan, Y.D. (2019) Prediction of S-Sulfenylation Sites Using Statistical Moments Based Features via Chou’s 5-Step Rule. International Journal of Peptide Research and Therapeutics (IJPRT), 19, 71-82. https://doi.org/10.1007/s10989-019-09931-2
Chen, Y. and Fan, X. (2019) Use Chou’s 5-Steps Rule to Reveal Active Compound and Mechanism of Shuangsheng Pingfei San on Idiopathic Pulmonary Fibrosis. Current Molecular Medicine, 19, 511-563.
Du, X., Diao, Y., Liu, H. and Li, S. (2019) MsDBP: Exploring DNA-Binding Proteins by Integrating Multi-Scale Sequence Information via Chou’s 5-Steps Rule. Journal of Proteome Research, 18, 3119-3132. https://doi.org/10.1021/acs.jproteome.9b00226
Dutta, A., Dalmia, A., R, A., Singh, K.K. and Anand, A. (2019) Using the Chou’s 5-Steps Rule to Predict Splice Junctions with Interpretable Bidirectional Long Short-Term Memory Networks. Computers in Biology and Medicine, 116, Article ID: 103558. https://doi.org/10.1016/j.compbiomed.2019.103558
Ehsan, A., Mahmood, M.K., Khan, Y.D., Barukab, O.M., Khan, S.A. and Chou, K.C. (2019) iHyd-PseAAC (EPSV): Identify Hydroxylation Sites in Proteins by Extracting Enhanced Position and Sequence Variant Feature via Chou’s 5-Step Rule and General Pseudo Amino Acid Composition. Current Genomics, 20, 124-133. https://doi.org/10.2174/1389202920666190325162307
Hussain, W., Khan, S.D., Rasool, N., Khan, S.A. and Chou, K.C. (2019) SPalmitoylC-PseAAC: A Sequence-Based Model Developed via Chou’s 5-Steps Rule and General PseAAC for Identifying S-Palmitoylation Sites in Proteins. Analytical Biochemistry, 568, 14-23. https://doi.org/10.1016/j.ab.2018.12.019
Hussain, W., Khan, Y.D., Rasool, N., Khan, S.A. and Chou, K.C. (2019) SPrenylC-PseAAC: A Sequence-Based Model Developed via Chou’s 5-Steps Rule and General PseAAC for Identifying S-Prenylation Sites in Proteins. Journal of Theoretical Biology, 468, 1-11. https://doi.org/10.1016/j.jtbi.2019.02.007
Jun, Z. and Wang, S.Y. (2019) Identify Lysine Neddylation Sites Using Bi-Profile Bayes Feature Extraction via the Chou’s 5-Steps Rule and General Pseudo Components. Current Genomics, 20, 592-601. https://doi.org/10.2174/1389202921666191223154629
Khan, S., Khan, M., Iqbal, N., Hussain, T., Khan, S.A. and Chou, K.C. (2019) A Two-Level Computation Model Based on Deep Learning Algorithm for Identification of piRNA and Their Functions via Chou’s 5-Steps Rule. Human Genetics, 19, 756-799. https://doi.org/10.1007/s10989-019-09887-3
Khan, Z.U., Ali, F., Khan, I.A., Hussain, Y. and Pi, D. (2019) iRSpot-SPI: Deep Learning-Based Recombination Spots Prediction by Incorporating Secondary Sequence Information Coupled with Physio-Chemical Properties via Chou’s 5-Step Rule and Pseudo Components. Chemometrics and Intelligent Laboratory Systems (CHEMOLAB), 189, 169-180. https://doi.org/10.1016/j.chemolab.2019.05.003
Lan, J., Liu, J., Liao, C., Merkler, D.J., Han, Q. and Li, J. (2019) A Study for Therapeutic Treatment against Parkinson’s Disease via Chou’s 5-Steps Rule. Current Topics in Medicinal Chemistry, 19, 2318-2333. https://doi.org/10.2174/1568026619666191019111528
Le, N.Q.K. (2019) iN6-methylat (5-Step): Identifying DNA N(6)-methyladenine Sites in Rice Genome Using Continuous Bag of Nucleobases via Chou’s 5-Step Rule. Molecular Genetics and Genomics: MGG, 294, 1173-1182. https://doi.org/10.1007/s00438-019-01570-y
Le, N.Q.K., Yapp, E.K.Y., Ho, Q.T., Nagasundaram, N., Ou, Y.Y. and Yeh, H.Y. (2019) iEnhancer-5Step: Identifying Enhancers Using Hidden Information of DNA Sequences via Chou’s 5-Step Rule and Word Embedding. Analytical Biochemistry, 571, 53-61. https://doi.org/10.1016/j.ab.2019.02.017
Le, N.Q.K., Yapp, E.K.Y., Ou, Y.Y. and Yeh, H.Y. (2019) iMotor-CNN: Identifying Molecular Functions of Cytoskeleton Motor Proteins Using 2D Convolutional Neural Network via Chou’s 5-Step Rule. Analytical Biochemistry, 575, 17-26. https://doi.org/10.1016/j.ab.2019.03.017
Liang, R., Xie, J., Zhang, C., Zhang, M., Huang, H., Huo, H., Cao, X. and Niu, B. (2019) Identifying Cancer Targets Based on Machine Learning Methods via Chou’s 5-Steps Rule and General Pseudo Components. Current Topics in Medicnal Chemistry, 19, 2301-2317. https://doi.org/10.2174/1568026619666191016155543
Liang, Y. and Zhang, S. (2019) Identifying DNase I Hypersensitive Sites Using Multi-Features Fusion and F-Score Features Selection via Chou’s 5-Steps Rule. Biophysical Chemistry, 253, Article ID: 106227. https://doi.org/10.1016/j.bpc.2019.106227
Liu, Z., Dong, W., Jiang, W. and He, Z. (2019) csDMA: An Improved Bioinformatics Tool for Identifying DNA 6 mA Modifications via Chou’s 5-Step Rule. Scientific Reports, 9, Article No. 13109. https://doi.org/10.1038/s41598-019-49430-4
Malebary, S.J., Rehman, M.S.U. and Khan, Y.D. (2019) iCrotoK-PseAAC: Identify Lysine Crotonylation Sites by Blending Position Relative Statistical Features According to the Chou’s 5-Step Rule. PLoS ONE, 14, e0223993. https://doi.org/10.1371/journal.pone.0223993
Nazari, I., Tahir, M., Tayari, H. and Chong, K.T. (2019) iN6-Methyl (5-step): Identifying RNA N6-methyladenosine Sites Using Deep Learning Mode via Chou’s 5-Step Rules and Chou’s General PseKNC. Chemometrics and Intelligent Laboratory Systems (CHEMOLAB), 19, 1-39. https://doi.org/10.1016/j.chemolab.2019.103811
Ning, Q., Ma, Z. and Zhao, X. (2019) dForml(KNN)-PseAAC: Detecting Formylation Sites from Protein Sequences Using K-Nearest Neighbor Algorithm via Chou’s 5-Step Rule and Pseudo Components. Journal of Theoretical Biology, 470, 43-49. https://doi.org/10.1016/j.jtbi.2019.03.011
Tahir, M., Tayara, H. and Chong, K.T. (2019) iDNA6mA (5-step rule): Identification of DNA N6-Methyladenine Sites in the Rice Genome by Intelligent Computational Model via Chou’s 5-Step Rule. CHEMOLAB, 189, 96-101. https://doi.org/10.1016/j.chemolab.2019.04.007
Wiktorowicz, A., Wit, A., Dziewierz, A., Rzeszutko, L., Dudek, D. and Kleczynski, P. (2019) Calcium Pattern Assessment in Patients with Severe Aortic Stenosis via the Chou’s 5-Steps Rule. Current Pharmaceutical Design, 25, 6-31. https://doi.org/10.2174/1381612825666190930101258
Yang, L., Lv, Y., Wang, S., Zhang, Q., Pan, Y., Su, D., Lu, Q. and Zuo, Y. (2019) Identifying FL11 Subtype by Characterizing Tumor Immune Microenvironment in Prostate Adenocarcinoma via Chou’s 5-Steps Rule. Genomics, 112, 1500-1515. https://doi.org/10.1016/j.ygeno.2019.08.021
Akbar, S., Rahman, A.U. and Hayat, M. (2020) cACP: Classifying Anticancer Peptides Using Discriminative Intelligent Model via Chou’s 5-Step Rules and General Pseudo Components. Chemometrics and Intelligent Laboratory (CHEMOLAB), 196, Article ID: 103912. https://doi.org/10.1016/j.chemolab.2019.103912
Akmal, M.A., Hussain, W., Rasool, N., Khan, Y.D., Khan, S.A. and Chou, K.C. (2020) Using Chou’s 5-Steps Rule to Predict O-Linked Serine Glycosylation Sites by Blending Position Relative Features and Statistical Moment. IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/TCBB.2020.2968441
Bouziane, H. and Chouarfia, A. (2020) Use of Chou’s 5-Steps Rule to Predict the Subcellular Localization of Gram-Negative and Gram-Positive Bacterial Proteins by Multi-Label Learning Based on Gene Ontology Annotation and Profile Alignment. Journal of Integrative Bioinformatics. https://doi.org/10.1515/jib-2019-0091
Charoenkwan, P., Schaduangrat, N., Nantasenamat, C., Piacham, T. and Shoombuatong, W. (2020) iQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou’s 5-Steps Rule and Informative Physicochemical Properties. International Journal of Molecular Sciences, 21, 75. https://doi.org/10.3390/ijms21010075
Charoenkwan, P., Schaduangrat, N., Nantasenamat, C., Piacham, T. and Shoombuatong, W. (2020) Correction: Shoombuatong, W., et al. iQSP: A Sequence-Based Tool for the Prediction and Analysis of Quorum Sensing Peptides via Chou’s 5-Steps Rule and Informative Physicochemical Properties. International Journal of Molecular Sciences, 21, 75. https://doi.org/10.3390/ijms21072629
Chen, Y. and Fan, X. (2020) Use of Chou’s 5-Steps Rule to Reveal Active Compound and Mechanism of Shuangshen Pingfei San on Idiopathic Pulmonary Fibrosis. Current Molecular Medicine, 20, 220-230. https://doi.org/10.2174/1566524019666191011160543
Dobosz, R., Mucko, J. and Gawinecki, R. (2020) Using Chou’s 5-Step Rule to Evaluate the Stability of Tautomers: Susceptibility of 2-[(Phenylimino)-methyl]-cyclohexane-1,3-diones to Tautomerization Based on the Calculated Gibbs Free Energies. Energies, 13, 183. https://doi.org/10.3390/en13010183
Du, L., Meng, Q., Jiang, H. and Li, Y. (2020) Using Evolutionary Information and Multi-Label Linear Discriminant Analysis to Predict the Subcellular Location of Multi-Site Bacterial Proteins via Chou’s 5-Steps Rule. IEEE Access, 8, 56452-56461. https://doi.org/10.1109/ACCESS.2020.2982160
Dutta, A., Dalmia, A., R, A., Singh, K.K. and Anand, A. (2020) Using the Chou’s 5-Steps Rule to Predict Splice Junctions with Interpretable Bidirectional Long Short-Term Memory Networks. Computers in Biology and Medicine, 116, Article ID: 103558. https://doi.org/10.1016/j.compbiomed.2019.103558
Ju, Z. and Wang, S.Y. (2020) Prediction of Lysine Formylation Sites Using the Composition of k-Spaced Amino Acid Pairs via Chou’s 5-Steps Rule and General Pseudo Components. Genomics, 112, 859-866. https://doi.org/10.1016/j.ygeno.2019.05.027
Kabir, M., Ahmad, S., Iqbal, M. and Hayat, M. (2020) iNR-2L: A Two-Level Sequence-Based Predictor Developed via Chou’s 5-Steps Rule and General PseAAC for Identifying Nuclear Receptors and Their Families. Genomics, 112, 276-285. https://doi.org/10.1016/j.ygeno.2019.02.006
Khan, Y.D., Amin, N., Hussain, W., Rasool, N., Khan, S.A. and Chou, K.C. (2020) iProtease-PseAAC(2L): A Two-Layer Predictor for Identifying Proteases and Their Types Using Chou’s 5-Step-Rule and General PseAAC. Analytical Biochemistry, 588, Article ID: 113477. https://doi.org/10.1016/j.ab.2019.113477
Lin, W., Xiao, X., Qiu, W. and Chou, K.C. (2020) Use Chou’s 5-Steps Rule to Predict Remote Homology Proteins by Merging Grey Incidence Analysis and Domain Similarity Analysis. Natural Science, 12, 181-198. https://doi.org/10.4236/ns.2020.123016
Lu, W., Song, Z., Ding, Y., Wu, H., Cao, Y. and Zhang, Y.L. (2020) Use Chou’s 5-Step Rule to Predict DNA-Binding Proteins with Evolutionary Information. BioMed Research International, 2020, Article ID: 6984045. https://doi.org/10.1155/2020/6984045
Nguyen, D., Ho-Quang, T., Nguyen Quoc Khanh, L., Dinh-Phan, V. and Ou, Y.Y. (2020) Use Chou’s 5-Steps Rule with Different Word Embedding Types to Boost Performance of Electron Transport Protein Prediction Model. IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/TCBB.2020.3010975
Pandey, R.P., Kumar, S., Ahmad, S., Vibhuti, A., Raj, V.S., Verma, A.K., Sharma, P. and Leal, E. (2020) Use Chou’s 5-Steps Rule to Evaluate Protective Efficacy Induced by Antigenic Proteins of Mycobacterium tuberculosis Encapsulated in Chitosan Nanoparticles. Life Sciences, 256, Article ID: 117961. https://doi.org/10.1016/j.lfs.2020.117961
Roy, T. and Bhattacharjee, P. (2020) A LabVIEW-Based Real-Time Modeling Approach via Chou’s 5-Steps Rule for Detection of Abnormalities in Cancer Cells. Gene Reports, 20, Article ID: 100788. https://doi.org/10.1016/j.genrep.2020.100788
So, C. and Yang, B. (2020) Use Chou’s 5-Step Rule to Classify Protein Modification Sites with Neural Network. Scientific Programming, 2020, Article ID: 8894633. https://doi.org/10.1155/2020/8894633
Song, C. and Yang, B. (2020) Use Chou’s 5-Step Rule to Classify Protein Modification Sites with Neural Network. Scientific Programming, 2020, Article ID: 8894633. https://doi.org/10.1155/2020/8894633
Vishnoi, S., Garg, P. and Arora, P. (2020) Physicochemical n-Grams Tool: A Tool for Protein Physicochemical Descriptor Generation via Chou’s 5-Step Rule. Chemical Biology & Drug Design, 95, 79-86. https://doi.org/10.1111/cbdd.13617
Vundavilli, H., Datta, A., Sima, C., Hua, J., Lopes, R. and Bittner, M. (2020) Using Chou’s 5-Steps Rule to Model Feedback in Lung Cancer. IEEE Journal of Biomedical and Health Informatics, 21, 1-24. https://doi.org/10.1109/JBHI.2019.2958042
Yang, L., Lv, Y., Wang, S., Zhang, Q., Pan, Y., Su, D., Lu, Q. and Zuo, Y. (2020) Identifying FL11 Subtype by Characterizing Tumor Immune Microenvironment in Prostate Adenocarcinoma via Chou’s 5-Steps Rule. Genomics, 112, 1500-1515. https://doi.org/10.1016/j.ygeno.2019.08.021
Zhang, S. and Xue, T. (2020) Use Chou’s 5-Steps Rule to Identify DNase I Hypersensitive Sites via Dinucleotide Property Matrix and Extreme Gradient Boosting. Molecular Genetics and Genomics: MGG, 295, 1431-1442. https://doi.org/10.1007/s00438-020-01711-8