计算分子生物学(英文)最新文献_第3页

Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa 结构宿主群体多类型出生死亡参数的推断及其在非洲艾滋病流行中的应用

计算分子生物学(英文) Pub Date : 2019-11-25 DOI: 10.4236/cmb.2019.94009

Hassan W. Kayondo, S. Mwalili, J. Mango

{"title":"Inferring Multi-Type Birth-Death Parameters for a Structured Host Population with Application to HIV Epidemic in Africa","authors":"Hassan W. Kayondo, S. Mwalili, J. Mango","doi":"10.4236/cmb.2019.94009","DOIUrl":"https://doi.org/10.4236/cmb.2019.94009","url":null,"abstract":"Human Immunodeficiency Virus (HIV) dynamics in Africa are purely characterised by sparse sampling of DNA sequences for individuals who are infected. There are some sub-groups that are more at risk than the general population. These sub-groups have higher infectivity rates. We came up with a likelihood inference model of multi-type birth-death process that can be used to make inference for HIV epidemic in an African setting. We employ a likelihood inference that incorporates a probability of removal from infectious pool in the model. We have simulated trees and made parameter inference on the simulated trees as well as investigating whether the model distinguishes between heterogeneous and homogeneous dynamics. The model makes fairly good parameter inference. It distinguishes between heterogeneous and homogeneous dynamics well. Parameter estimation was also performed under sparse sampling scenario. We investigated whether trees obtained from a structured population are more balanced than those from a non-structured host population using tree statistics that measure tree balance and imbalance. Trees from non-structured population were more balanced basing on Colless and Sackin indices.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47325941","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}

引用次数: 2

Computational Study of the Chemical Reactivity and Bioactivity Rates of Marine Peptides Hemiasterlin and Its A and B Derivatives Used in the Cancer Treatment through Conceptual Density Functional Theory 应用概念密度泛函理论计算癌症治疗中海洋肽半星号及其A、B衍生物的化学反应性和生物活性

计算分子生物学(英文) Pub Date : 2019-11-25 DOI: 10.4236/cmb.2019.94008

N. Flores-Holguín, J. Frau, D. Glossman-Mitnik

引用次数: 2

Molecular Docking and Pharmacological Property Analysis of Phytochemicals from Clitoria ternatea as Potent Inhibitors of Cell Cycle Checkpoint Proteins in the Cyclin/CDK Pathway in Cancer Cells 癌症细胞周期蛋白/CDK通路细胞周期检查点蛋白的分子对接及药理性质分析

计算分子生物学(英文) Pub Date : 2019-08-09 DOI: 10.4236/cmb.2019.93007

Asad Ullah, Nazmul Islam Prottoy, Yusha Araf, S. Hossain, Bishajit Sarkar, Ananna Saha

{"title":"Molecular Docking and Pharmacological Property Analysis of Phytochemicals from Clitoria ternatea as Potent Inhibitors of Cell Cycle Checkpoint Proteins in the Cyclin/CDK Pathway in Cancer Cells","authors":"Asad Ullah, Nazmul Islam Prottoy, Yusha Araf, S. Hossain, Bishajit Sarkar, Ananna Saha","doi":"10.4236/cmb.2019.93007","DOIUrl":"https://doi.org/10.4236/cmb.2019.93007","url":null,"abstract":"Cancer comprises a group of diseases which are involved in the aberrant growth of the cells causing disruption of normal body function. Due to the lack of proper sophisticated treatments this nasty disease leads to the death of most of the patients affected with it. Moreover, treatments like chemotherapy involve other post-treatment complications which make them unfavorable for extended use. Medicinal plants possess many phytochemicals of great therapeutic value and many of them are effective in killing cancer cells. These compounds working by variety of mechanisms and in most of the cases exhibit their anticancer potentiality by inhibiting many proteins involved in cell growth and division. Molecular docking is a computational approach which facilitates the finding of the best molecule from a group which may bind with the highest affinity with the intended target by providing a virtual biological system. This process works on the basis of specific algorithm and involves scoring function to rank the molecules that fit with the target. This study has been designed to investigate the potentiality of four phytochemicals from Clitoria ternatea—Kaempferol, Myricetin, P-Hydroxycinnamic acid and Quercetin as inhibitors of two cell cycle checkpoint proteins—Cyclin Dependent Kinase-2 (CDK-2) and Cyclin Dependent Kinase-6 (CDK-6) in Cyclin/CDK pathway. Quercetin and Myricetin docked with higher affinity with CDK-2 and CDK-6 respectively. Drug likeness property analysis and ADME/T test impose computational approach to investigate physicochemical and pharmacological properties of candidate drug molecules. P-Hydroxycinnamic acid performed well in both drug likeness property analysis and ADME/T than Quercetin and Myricetin. So, P-Hydroxycinnamic acid is the best finding of this experiment.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44144227","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}

引用次数: 20

Studies of the Chemical Reactivity of a Series of Rhodanine Derivatives by Approaches to Quantum Chemistry 一系列罗丹宁衍生物化学反应性的量子化学研究

计算分子生物学(英文) Pub Date : 2019-08-09 DOI: 10.4236/CMB.2019.93005

W. Coulibaly, Jean Stéphane N’dri, M. Koné, C. D. Dago, Christelle N’ta Ambeu, J. Bazureau, N. Ziao

引用次数: 9

DFT Study, Linear and Nonlinear Multiple Regression in the Prediction of HDAC7 Inhibitory Activities on a Series of Hydroxamic Acids DFT研究、线性和非线性多元回归预测HDAC7对一系列羟肟酸的抑制活性

计算分子生物学(英文) Pub Date : 2019-08-09 DOI: 10.4236/cmb.2019.93006

Doh Soro, Lynda Ekou, B. Ouattara, M. Koné, T. Ekou, N. Ziao

引用次数: 2

Chemical Reactivity Properties, Drug-Likeness Features and Bioactivity Scores of the Cholecystokinin Peptide Hormone 胆囊收缩素肽激素的化学反应性、药物相似特征及生物活性评分

计算分子生物学(英文) Pub Date : 2019-06-28 DOI: 10.4236/CMB.2019.92004

N. Flores-Holguín, J. Frau, D. Glossman-Mitnik

引用次数: 11

Conceptual Density Functional Theory Study of the Chemical Reactivity Properties and Bioactivity Scores of the Leu-Enkephalin Opioid Peptide Neurotransmitter Leu-Enkephalin阿片肽神经递质化学反应特性和生物活性评分的概念密度泛函理论研究

计算分子生物学(英文) Pub Date : 2019-02-22 DOI: 10.4236/CMB.2019.91002

J. Frau, N. Flores-Holguín, D. Glossman-Mitnik

{"title":"Conceptual Density Functional Theory Study of the Chemical Reactivity Properties and Bioactivity Scores of the Leu-Enkephalin Opioid Peptide Neurotransmitter","authors":"J. Frau, N. Flores-Holguín, D. Glossman-Mitnik","doi":"10.4236/CMB.2019.91002","DOIUrl":"https://doi.org/10.4236/CMB.2019.91002","url":null,"abstract":"The SMD solvation model (Solvation Model based on the Density) and eight density functionals, CAM-B3LYP, LC-ωPBE, M11, MN12SX, N12SX, ωB97, ωB97X, and ωB97XD, were assessed in link with the Def2TZVP basis set for the calculation of the structure of the Leu-Enkephalin Opioid Peptide Neurotransmitter as well as their molecular properties. Through the Conceptual Density Functional Theory (CDFT), the entire chemical descriptors for the system were calculated. The active regions of the molecules necessary for electrophilic, nucleophilic and radical attacks were chosen through linking them with the corresponding Fukui functions. Furthermore, the prediction of the pKa value for the peptide is done with great accuracy as well as the ability of the studied molecule in acting as an efficient inhibitor of the formation of Advanced Glycation Endproducts (AGEs), which comprises of a useful knowledge for the development of drugs for preventing Alzheimer, Diabetes and Parkinson diseases. Lastly, the bioactivity scores for the studied peptides are predicted via various methodologies.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2019-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44383557","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}

引用次数: 10

Bacterial Heavy Metal Resistance Genes and Bioremediation Potential 细菌重金属抗性基因及其生物修复潜力

计算分子生物学(英文) Pub Date : 2019-02-22 DOI: 10.4236/CMB.2019.91001

H. Johnson, Hyuk Cho, M. Choudhary

引用次数: 15

Spontaneous Unfolding and Refolding of Plantaricin α-Helix in Molecular Dynamics Simulation Plantaricinα-螺旋在分子动力学模拟中的自发展开和再折叠

计算分子生物学(英文) Pub Date : 2019-02-22 DOI: 10.4236/cmb.2019.91003

Shaomin Yan, Guang Wu

引用次数: 0

Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains. DOPC脂质双层分子动力学模拟:碳氢链Lennard-Jones参数的影响。

计算分子生物学(英文) Pub Date : 2012-09-01 DOI: 10.4236/cmb.2012.23007

Anping Liu, Xiaoyang Qi

引用次数: 10