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An Integrative Computational Approach for Design and Evaluation of Novel [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole Analogues as Dual-Action Anti-Retroviral and Anti-Bacterial Agents: Insights into Rational Drug Design Strategies 设计和评估新型[1,2,4]三唑并[3,4-b][1,3,4]噻二唑类似物作为抗逆转录病毒和抗菌双重作用药物的综合计算方法：对合理药物设计策略的启示
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-08-09 DOI: 10.1142/s2737416524500418
Rahul Ghosh, Swastika Ganguly
{"title":"An Integrative Computational Approach for Design and Evaluation of Novel [1,2,4]triazolo[3,4-b][1,3,4]thiadiazole Analogues as Dual-Action Anti-Retroviral and Anti-Bacterial Agents: Insights into Rational Drug Design Strategies","authors":"Rahul Ghosh, Swastika Ganguly","doi":"10.1142/s2737416524500418","DOIUrl":"https://doi.org/10.1142/s2737416524500418","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141925625","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Natural Products from Brazilian Biodiversity Explored as Anti-EBV Drug Candidates: In-Silico Database Mining, Docking Computations, Molecular Dynamics, and DFT Calculations 探索巴西生物多样性中的天然产品作为抗乙型脑炎病毒候选药物：硅内数据库挖掘、对接计算、分子动力学和 DFT 计算
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-12 DOI: 10.1142/s2737416524500327
Alaa M. A. Hassan, Peter A. Sidhom, G. Mekhemer, Mohamed A. El-Tayeb, Mohamed-Elamir F. Hegazy, Mahmoud A. A. Ibrahim
{"title":"Natural Products from Brazilian Biodiversity Explored as Anti-EBV Drug Candidates: In-Silico Database Mining, Docking Computations, Molecular Dynamics, and DFT Calculations","authors":"Alaa M. A. Hassan, Peter A. Sidhom, G. Mekhemer, Mohamed A. El-Tayeb, Mohamed-Elamir F. Hegazy, Mahmoud A. A. Ibrahim","doi":"10.1142/s2737416524500327","DOIUrl":"https://doi.org/10.1142/s2737416524500327","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141652643","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
SGCAL: An algorithm to identify sensitive gene combinations in the mouse osteoblast gene network SGCAL：识别小鼠成骨细胞基因网络中敏感基因组合的算法
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-12 DOI: 10.1142/s2737416524500352
Nan Chen, Yaru Chen, Yongfei Hu, Haohua Wang
{"title":"SGCAL: An algorithm to identify sensitive gene combinations in the mouse osteoblast gene network","authors":"Nan Chen, Yaru Chen, Yongfei Hu, Haohua Wang","doi":"10.1142/s2737416524500352","DOIUrl":"https://doi.org/10.1142/s2737416524500352","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141654292","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Persistent Path Homology for Quantitative Analysis of Carboranes 用于碳硼烷定量分析的持久性路径同源性
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-12 DOI: 10.1142/s2737416524500339
Bingxu Wang, Mingzheng Zhang, Feng Pan
{"title":"Persistent Path Homology for Quantitative Analysis of Carboranes","authors":"Bingxu Wang, Mingzheng Zhang, Feng Pan","doi":"10.1142/s2737416524500339","DOIUrl":"https://doi.org/10.1142/s2737416524500339","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141653429","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Inhibition of β-lactamase by Novel Benzothiazole-Coupled Azetidinone Derivatives: A Comprehensive Study Using an In-silico and In-vitro Approaches Against Multi Drug Resistant Bacteria 新型苯并噻唑偶联氮杂环丁酮衍生物对β-内酰胺酶的抑制作用：采用体内和体外方法对多重耐药菌进行综合研究
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-12 DOI: 10.1142/s2737416524500340
Gupta Dheeraj Rajesh, Abel John Koshy, Sadanand Dangari Akshay, Prarambh S. R. Dwivedi, Harsha Ashtekar, Niyas Rehman, Pankaj Kumar
{"title":"Inhibition of β-lactamase by Novel Benzothiazole-Coupled Azetidinone Derivatives: A Comprehensive Study Using an In-silico and In-vitro Approaches Against Multi Drug Resistant Bacteria","authors":"Gupta Dheeraj Rajesh, Abel John Koshy, Sadanand Dangari Akshay, Prarambh S. R. Dwivedi, Harsha Ashtekar, Niyas Rehman, Pankaj Kumar","doi":"10.1142/s2737416524500340","DOIUrl":"https://doi.org/10.1142/s2737416524500340","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141655195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular Docking, Quantum Mechanics and Molecular Dynamics Simulation of Anti-CAD Drugs Against High-Risk Xanthine Dehydrogenase Variants Associated with Oxidative Stress Pathways 针对与氧化应激途径相关的高风险黄嘌呤脱氢酶变体的抗 CAD 药物的分子对接、量子力学和分子动力学模拟
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-05 DOI: 10.1142/s2737416524500315
V. Janakiraman, M. Sudhan, Sheikh F. Ahmad, S. Attia, T. Emran, Shiek Ssj Ahmed
{"title":"Molecular Docking, Quantum Mechanics and Molecular Dynamics Simulation of Anti-CAD Drugs Against High-Risk Xanthine Dehydrogenase Variants Associated with Oxidative Stress Pathways","authors":"V. Janakiraman, M. Sudhan, Sheikh F. Ahmad, S. Attia, T. Emran, Shiek Ssj Ahmed","doi":"10.1142/s2737416524500315","DOIUrl":"https://doi.org/10.1142/s2737416524500315","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141674244","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reactions of hydroperoxyl radicals (HO2) with oxygenated aromatic bio-oil model compounds 氢过氧自由基 (HO2) 与含氧芳香族生物油模型化合物的反应
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-05 DOI: 10.1142/s2737416524500303
Mubarak Al-Kwradi, Ali Huseein Al-Jefri, M. Altarawneh
{"title":"Reactions of hydroperoxyl radicals (HO2) with oxygenated aromatic bio-oil model compounds","authors":"Mubarak Al-Kwradi, Ali Huseein Al-Jefri, M. Altarawneh","doi":"10.1142/s2737416524500303","DOIUrl":"https://doi.org/10.1142/s2737416524500303","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141676995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Impact of Centrality Measures in Protein–Protein Interaction Networks: Tools, Databases, Challenges and Future Directions 蛋白质-蛋白质相互作用网络中中心性测量的影响：工具、数据库、挑战和未来方向
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-03 DOI: 10.1142/s2737416524400076
Nirmala Parisutham
{"title":"The Impact of Centrality Measures in Protein–Protein Interaction Networks: Tools, Databases, Challenges and Future Directions","authors":"Nirmala Parisutham","doi":"10.1142/s2737416524400076","DOIUrl":"https://doi.org/10.1142/s2737416524400076","url":null,"abstract":"Analyzing protein–protein interaction (PPI) networks using machine learning and deep learning algorithms, alongside centrality measures, holds paramount importance in understanding complex biological systems. These advanced computational techniques enable the extraction of valuable insights from intricate network structures, shedding light on the functional relationships between proteins. By leveraging AI-driven approaches, researchers can uncover key regulatory mechanisms, identify critical nodes within the network and predict novel protein interactions with high accuracy. Ultimately, this integration of computational methodologies enhances our ability to comprehend the dynamic behavior of biological systems at a molecular level, paving the way for advancements in drug discovery, disease understanding and personalized medicine. This review paper starts by outlining various popular available PPI network databases and network centrality calculation tools. A thorough classification of various centrality measures has been identified. It primarily delves into the centrality-driven discoveries within PPI networks in biological systems and suggests using edge centrality measures and a hybrid version of node and edge centrality measures in machine learning algorithms and deep learning algorithms to predict hidden knowledge much more effectively.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141681225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Feature Selection and Classification Technique for Predicting Lymph Node Metastasis of Papillary Thyroid Carcinoma 预测甲状腺乳头状癌淋巴结转移的特征选择和分类技术
IF 2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-07-03 DOI: 10.1142/s2737416524400064
Dan Wu, Zhuang Yan, Guoliang Liao, Lin Han, Ke Chen, Cheng Li, Zhan Hua, Jiangli Lin
{"title":"Feature Selection and Classification Technique for Predicting Lymph Node Metastasis of Papillary Thyroid Carcinoma","authors":"Dan Wu, Zhuang Yan, Guoliang Liao, Lin Han, Ke Chen, Cheng Li, Zhan Hua, Jiangli Lin","doi":"10.1142/s2737416524400064","DOIUrl":"https://doi.org/10.1142/s2737416524400064","url":null,"abstract":"Papillary thyroid carcinoma (PTC) is typically an indolent cancer, yet a minority of cases develop lymph node metastasis. Due to the unclear mechanisms of lymph node metastasis, a considerable number of patients undergo unnecessary surgeries. Currently, the identification of key genetic biomarkers in high-dimensional data presents a significant challenge, thereby limiting research progress in this area. Here, we proposed a hybrid filter-wrapper feature selection strategy for core factor detection and developed MethyAE, a metastasis prediction model based on DNA methylation, utilizing an end-to-end learning auto-encoder. 46 methylated CpG sites were successfully identified as crucial biomarkers for lymph node metastasis. Leveraging 447 PTC samples from the Cancer Genome Atlas (221 with metastasis, 226 without), the MethyAE model achieves 88.9% accuracy and a recall rate of 88.6% in predicting lymph node metastasis, outperforming commonly used machine learning methods like logistic regression and random forest. Furthermore, the MethyAE model exhibits favorable performance in DNA methylation data from colon cancer, bladder cancer, and breast cancer. To the best of our knowledge, this is the first attempt to predict PTC lymph node metastasis through DNA methylation, offering pivotal decision-making criteria for avoiding unnecessary surgeries and selecting appropriate treatment plans for a substantial cohort of PTC patients.","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141683762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring Plant-Derived Bioactive Compounds in Olea Europaea L. Leaves as Potent Inhibitors of PTP-1B Using an In silico Approach 利用硅学方法探索油橄榄叶中植物提取的生物活性化合物作为 PTP-1B 的强效抑制剂
IF 2.2 4区 化学
Journal of Computational Biophysics and Chemistry Pub Date : 2024-06-10 DOI: 10.1142/s2737416524500248
N. Shridhar Deshpande, Shrutesh Wagh, Abhishek Prakash Sharma, Amgoth Ramesh, Mahindra, Lavanya, B.S. Moksha, Divyashree, Disha, Sheshagiri R. Dixit, Deepshikha Singh, Durgesh Paresh Bidye, B. C. Revanasiddappa
{"title":"Exploring Plant-Derived Bioactive Compounds in Olea Europaea L. Leaves as Potent Inhibitors of PTP-1B Using an In silico Approach","authors":"N. Shridhar Deshpande, Shrutesh Wagh, Abhishek Prakash Sharma, Amgoth Ramesh, Mahindra, Lavanya, B.S. Moksha, Divyashree, Disha, Sheshagiri R. Dixit, Deepshikha Singh, Durgesh Paresh Bidye, B. C. Revanasiddappa","doi":"10.1142/s2737416524500248","DOIUrl":"https://doi.org/10.1142/s2737416524500248","url":null,"abstract":"","PeriodicalId":15603,"journal":{"name":"Journal of Computational Biophysics and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.2,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141364511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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