计算分子生物学(英文)最新文献

{"title":"Antibody-Like Phosphorylation Sites. Theme for Studies of Cancer, Aging and Evolution","authors":"J. Kubrycht, K. Sigler","doi":"10.4236/cmb.2022.121004","DOIUrl":"https://doi.org/10.4236/cmb.2022.121004","url":null,"abstract":"Sequence similarities were found between protein and DNA sequences encoding certain part of conserved variable immunoglobulin domains (i.e. conserved IgV) and phosphorylation sites. Hypermutation motifs were then indicated in the majority of the corresponding non-IgV nucleotide sequences. According to database confirmations or double prediction of phosphorylation sites, 80% of the selected human and mouse IgV-related phosphorylation sites or their highly probable candidates exhibited substrate relationship to atax-ia-telangiectasia-mutated kinase known as ATM. In accordance with litera-ture data, inactivation of ATM by mutations can participate in the mechan-isms of carcinogenesis, neurodegeneration and possibly also in aging. In agreement with this relationship, some of the selected IgV-/ATM-related segments formed molecules specifically involved in carcinogenesis. The selected IgV-related sequence segments were also similar to certain segments of higher plants containing immunoglobulin-like repeats and related regions. Bioinformatic analysis of some selected plant sequences then indicated the presence of catalytic domains composing serine/threonine/tyrosine recep-tor/receptor-like kinases, which are considered important structures for evolution of very early and part of later Ig-domain-related immunity. The ana-lyzed conserved domain similarities also suggested certain interesting structural and phylogenic relationships, which need to be further investigated. This review in fact briefly summarizes the findings on the subject from the last twenty years.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70445015","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary Relationship of Protein Sequences of SARS-CoV-2 and Other Viruses through Chaos Game Representation","authors":"Matthew D. Hill, Kevin E. Simmons, D. C. Sengupta","doi":"10.4236/cmb.2022.123008","DOIUrl":"https://doi.org/10.4236/cmb.2022.123008","url":null,"abstract":"","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70444941","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global Genomic Variations of Pathogenic Bacteria Salmonella Reading","authors":"Woo Hyung Lee, Ye-Rin Jeon, J. Chung, W. J. Shim, Min Jae Shin, Seong Gab Han, S. Baek, James Kim, Jaewoo Kim, P. Chung","doi":"10.4236/cmb.2021.113004","DOIUrl":"https://doi.org/10.4236/cmb.2021.113004","url":null,"abstract":"US Centers for Disease Control and Prevention (CDC) estimates food-borne pathogenic Salmonella bacteria cause about 1.35 million infections, 26,500 hospitalizations, and 420 deaths in the U.S. every year. Outbreaks of multidrug-resistant Salmonella Reading linked mainly to raw turkey products and alfalfa sprouts have accounted for human illness including mortality. Therefore, we downloaded and compared genome sequences of 897 Salmonella Reading isolated from 27 resources in 11 countries at 21 year-points from the National Center for Biotechnology Information database. Isolates were clustered into 10 clades which consisted of 3 major and 7 minor or single node clades. Although 3 major clades included both Europe and American isolates, one clade consisted of 605 North American isolates out of 614 isolates. Evolutionary distance is more related to the continent than the source of isolation. The host source, continent (North America and Europe) and phylogenetic clade were related to the prevalence of isolates encoding Antimicrobial Resistance Genes (ARGs). Prevalence of prophages was greater in bovine and swine isolates than poultry and human isolates and the least prevalence was found in human isolates. Between continents, the prevalence of phage was greater in North American isolates than European. The diversity of virulence factors in swine isolates differed from poultry isolate while no difference was found among continents. In conclusion, evolutionary distance is related to isolation host source rather than the continent, and genome features were distinguished by host and cluster. Our genomic analysis implies that Salmonella Reading evolved indeHow to cite this paper: Lee, W.H., Jeon, Y., Chung, J.S., Shim, W.J., Shin, M.J., Han, S.G., Baek, S., Kim, J., Kim, J. and Chung, P.S. (2021) Global Genomic Variations of Pathogenic Bacteria Salmonella Reading. Computational Molecular Bioscience, 11, 57-68. https://doi.org/10.4236/cmb.2021.113004 Received: September 1, 2021 Accepted: September 27, 2021 Published: September 30, 2021 Copyright © 2021 by author(s) and Scientific Research Publishing Inc. This work is licensed under the Creative Commons Attribution International License (CC BY 4.0). http://creativecommons.org/licenses/by/4.0/ Open Access","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70444665","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reinforcement Learning of Molecule Optimization with Bayesian Neural Networks","authors":"Wei Hu","doi":"10.4236/cmb.2021.114005","DOIUrl":"https://doi.org/10.4236/cmb.2021.114005","url":null,"abstract":"Creating new molecules with desired properties is a fundamental and chal-lenging problem in chemistry. Reinforcement learning (RL) has shown its utility in this area where the target chemical property values can serve as a reward signal. At each step of making a new molecule, the RL agent learns se-lecting an action from a list of many chemically valid actions for a given molecule, implying a great uncertainty associated with its learning. In a traditional implementation of deep RL algorithms, deterministic neural networks are typically employed, thus allowing the agent to choose one action from one sampled action at each step. In this paper, we proposed a new strategy of applying Bayesian neural networks to RL to reduce uncertainty so that the agent can choose one action from a pool of sampled actions at each step, and inves-tigated its benefits in molecule design. Our experiments suggested the Bayesian approach could create molecules of desirable chemical quality while maintained their diversity, a very difficult goal to achieve in machine learning of molecules. We further exploited their diversity by using them to train a generative model to yield more novel drug-like molecules, which were absent in the training molecules as we know novelty is essential for drug candidate molecules. In conclusion, Bayesian approach could offer a balance between exploitation and exploration in RL, and a balance between optimization and diversity in molecule design.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70444670","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Human RhCG Ammonia Conduction Mechanism","authors":"Henry J. Hoyhtya, H. Koster, M. M. Christiansen, U. Akgun","doi":"10.4236/cmb.2020.103006","DOIUrl":"https://doi.org/10.4236/cmb.2020.103006","url":null,"abstract":"The structural differences between E. coli AmtB and the human RhCG as well as the Rh50 from Nitrosomonas europaea suggest different ammonia conduction mechanisms for the AmtB and the Rh proteins. This study investigates the mechanism differences by using molecular dynamics simulations on RhCG and Rh50NE structures. Unlike AmtB the Rh proteins lack the aromatic cage at the bottom of the periplasmic vestibule. This report establishes the periplasmic Glu residue as the N H +4 binding site for Rh proteins, and the two Phe residues at the entrance of the pore as the NH3 binding site. The N H +4 molecule pushed by another ammonium releases one of its protons on its way to the phenyl gate. This study also discovers that, unlike AmtB, the Rh protein pores allow water molecules, which eventually facilitates the NH3 conduction from periplasm to cytoplasm.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43087576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Similarity Studies of Corona Viruses through Chaos Game Representation.","authors":"Dipendra C Sengupta, Matthew D Hill, Kevin R Benton, Hirendra N Banerjee","doi":"10.4236/cmb.2020.103004","DOIUrl":"10.4236/cmb.2020.103004","url":null,"abstract":"<p><p>The novel coronavirus (SARS-COV-2) is generally referred to as Covid-19 virus has spread to 213 countries with nearly 7 million confirmed cases and nearly 400,000 deaths. Such major outbreaks demand classification and origin of the virus genomic sequence, for planning, containment, and treatment. Motivated by the above need, we report two alignment-free methods combing with CGR to perform clustering analysis and create a phylogenetic tree based on it. To each DNA sequence we associate a matrix then define distance between two DNA sequences to be the distance between their associated matrix. These methods are being used for phylogenetic analysis of coronavirus sequences. Our approach provides a powerful tool for analyzing and annotating genomes and their phylogenetic relationships. We also compare our tool to ClustalX algorithm which is one of the most popular alignment methods. Our alignment-free methods are shown to be capable of finding closest genetic relatives of coronaviruses.</p>","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7497811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38399841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVID-2019 Genome Sequence Analysis: Phylogenetic Molecular Evolution and Docking of Structural Modelling of Receptor Binding Domain of S Protein in Active Site of ACE2","authors":"Abaysew Ayele, Baba Abdissa, Dereje Taye, Bereket Yemane, R. Majumdar","doi":"10.4236/cmb.2020.103007","DOIUrl":"https://doi.org/10.4236/cmb.2020.103007","url":null,"abstract":"Meanwhile the outbreak of the Covid-19 since December, 2019 in China, it has killed more than a hundred thousand of people of all ages and sex across the globe in a short span of time. On the bases of this study the nearest family member of the virus and its receptor binding domain of S protein including its model structure and function of its active sites were naked through Multiple Sequence Alignment, modelling and molecular docking software accordingly its repository genome databases. The virus was genetically associated and molecular evolutionary related with (RaTG13) and it scores 96.12% homology with 99% query coverage followed by bat-SL-CoVZC45 and bat-SL-CoVZXC21 notch 89.12% and 88.65% respectively. However, SARS and MERS corona type virus those outbreak earlier respectively less likely family members of 2019-nCoV. Though the virus has a close genetic association with those previous SARS coronaviruses, and certainly the spike protein used as a binding receptor to fight against human receptor protein of ACE 2, but on the basis of FRODOC and HDOCK server analysis multi favorable active sites of S protein was discovered such GLN493 shown as a finest key in both model and possessed a unique traits on it resulting unexpected rate of transmission and number of people died while compared to the previous one. TYR500, ASN501, GLN498 and others residues preferably contemplate site also. In particular, the diversity of the virus in the world may be due to the genome structure of the virus and S gene changed over the time, across the world against to host of human genetic diversity, which may be more robust, and may be a new and unique feature. This is because it is characterized close to contact with distance divergence between wild type novel coronavirus which was risen from China against to the genomes from Lebanon, India, Italy, and USA and so on. Thus, the World Health Organization and its researchers should focus on immunologic research and effective drug and vaccine development that will help to address the epidemiology of the virus, which can provide a long-term solution.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41314465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Investigation of the Interaction of Anti-Influenza Drugs with CoVID-19 Protein","authors":"Kassim F. Adebambo","doi":"10.4236/cmb.2020.102003","DOIUrl":"https://doi.org/10.4236/cmb.2020.102003","url":null,"abstract":"Coronavirus (CoVID-19) is a new outbreak of coronavirus disease which started in the Wuhan, China, the spread of this virus has now reached a global stage, urgent need is therefore needed to find new drug molecules which can either be used as a first aid intervention or slow down the multiplication rate of the virus within the system. In order to address this, this research looked into the existing antiviral drugs and screened them for their inhibitory properties towards the CoVID-19 protein. Recently, the crystal structure of the CoVID-19 (6LU7) protein has been established, this gives us the possible drug target site in CoVID-19. The binding affinity of the six compounds was screened using MOE (Molecular Operating Environment) software, four compounds (Zanamivir, Peramivir, Rimantidine, and Oseltamivir) out these six compounds have been approved by the Food Drug and Administration (FDA). The molecular docking calculation, Higher Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO) calculation were used to hypothesise the bioactivity of the FDA approved drug against the CoVID-19 protein. The calculation showed that Pimodivir tops the list of the anti influenza drug which can be used as first aid treatment for patient. Apart from Pimodivir, Laninamivir Octanoate is also a very good drug which might be used to inhibit CoVID-19 protein. It was also discovered that based on binding property of Rimantadine, it might be suitable for Fragment Based Drug Design (FBDD) approach which might lead to the discovery of completely new drug entity. Stability of the new protein structure was studied using GROMACS molecular dynamic simulation software. The results showed that the stability of the protein structure was achieved over a range of time, this confirmed that 6LU7 crystal structure might be a suitable protein crystal structure suitable for the development of new drug towards the treatment of CoVID-19. Finally, based on the molecular docking result, Pimodivir and Laninamivir Octanoate might be useful in the treatment of infected patient.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46927330","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Conserved Immunoglobulin Domain Similarities of Higher Plant Proteins","authors":"J. Kubrycht, K. Sigler","doi":"10.4236/cmb.2020.101002","DOIUrl":"https://doi.org/10.4236/cmb.2020.101002","url":null,"abstract":"The traces of immunoglobulin domain similarities were searched in sequences of higher plants using bioinformatic tools to look for possible early phylogenic structural relationships. 280 thousand sequence IDs, obtained by sixteen types of primary BLAST searches, were differently processed by seventeen selection procedures and an anti-redundant sequence-related approach using JavaScript, PHP, Windows programs and conserved domain searches by means CDD. The resulting seventeen sets of records describing conserved domain similarities of 1323 different sequence IDs yielded a set of next generation (final set) comprising forty-nine records containing superior (“non-refutable”) conserved immunoglobulin domain similarities. The selected sets and their subsets were mapped and subsequently statistically compared with respect to immunoglobulin-related as well as other reciprocal domain linkages. The list of frequently occurring conserved domain similarities concerned first of all domains important for plant and metazoan immunity, e.g. tyrosine kinases accompanying variable immunoglobulin domains in early Metazoa, toll-like receptors, lectin and leucine-rich repeat domains. Detailed description of immunoglobulin domain similarities occurring in the final set was completed by fold analysis of the restricted segments. The data were then discussed with respect to i) immunoglobulin fold evolution, ii) possible structural importance of domains cd14066 (IRAK) and PLN00113 (LRR-associated kinase) for deep evolution of catalytic serine/threonine/tyrosine kinase domains, iii) interatomic, structural and specificity standpoints and iv) traces of antibody-like phosphorylation sites described in our previous paper.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49494897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular Docking and Conceptual DFT-Based Study of Some Potential SARS-CoV-2 Inhibitors","authors":"N. Flores-Holguín, D. Glossman-Mitnik","doi":"10.4236/cmb.2020.104008","DOIUrl":"https://doi.org/10.4236/cmb.2020.104008","url":null,"abstract":"Nowadays, the main effort of the scientific community is focused on the search of specific drugs for the inhibition of the Severe Acute Respiratory Syndrome—Coronavirus 2 (SARS-CoV-2), which is responsible for the Coro-navirus Disease 19 or COVID-19. With the same objective in mind, a Molecular Docking study was performed in this work in order to discover information about some antiviral drugs of common use as protease inhibitors. As a complement of this research, a chemical reactivity study of these potential drugs was done with the aim of finding a relationship between the inhibition ability and the chemical reactivity. The results presented in this research constitute one of the first predictions aimed to identify the best potential compounds for this purpose while at the same time verifying the validity of the employed theoretical and computational methodology. By means of the analysis of the number of hydrogen bonds as well as the binding energies coming from the Molecular Docking study, it can be said that Telaprevir, Nelfinavir and Indinavir have the highest probability of success as potential inhibitors of SARS-CoV-2.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70444618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}