Pub Date : 2023-12-13DOI: 10.1080/07391102.2023.2293263
Ahmed Samir, Wael M. Elshemey, Abdo A. Elfiky
The interaction between the C-terminal domain (CTD) of the polymerase acidic (PA) component of three Flu A RNA polymerases of different origins and three heptad repeats from human polymerase II CTD...
{"title":"Molecular dynamics simulations and MM-GBSA reveal a novel small molecule against Flu A RNA-dependent RNA polymerase","authors":"Ahmed Samir, Wael M. Elshemey, Abdo A. Elfiky","doi":"10.1080/07391102.2023.2293263","DOIUrl":"https://doi.org/10.1080/07391102.2023.2293263","url":null,"abstract":"The interaction between the C-terminal domain (CTD) of the polymerase acidic (PA) component of three Flu A RNA polymerases of different origins and three heptad repeats from human polymerase II CTD...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629365","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}
Pub Date : 2023-12-13DOI: 10.1080/07391102.2023.2293277
Mohammad Raish, Ajaz Ahmad, Shahnawaz Khan, Mohd Abul Kalam
The current study used the major target protein lactate dehydrogenase Cryptosporidium parvum to identify potential binders. Our approach was a comprehensive three-step screening of 2,569 natural co...
{"title":"Molecular insights into anti-Protozoal action of natural compounds against Cryptosporidium parvum: a molecular simulation study","authors":"Mohammad Raish, Ajaz Ahmad, Shahnawaz Khan, Mohd Abul Kalam","doi":"10.1080/07391102.2023.2293277","DOIUrl":"https://doi.org/10.1080/07391102.2023.2293277","url":null,"abstract":"The current study used the major target protein lactate dehydrogenase Cryptosporidium parvum to identify potential binders. Our approach was a comprehensive three-step screening of 2,569 natural co...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138680876","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2292297
Jehoshaphat Oppong Mensah, Aaron Boakye, Michael Laryea, Edward Ntim Gasu, Lawrence Sheringham Borquaye
Antimicrobial resistance is a pressing global health concern, underscoring the need for alternative treatments. Antimicrobial peptides (AMPs) have shown promise in this regard, with maximin 1 being...
{"title":"Molecular insights into the differential membrane targeting of maximin 1 in prokaryotic and eukaryotic cells","authors":"Jehoshaphat Oppong Mensah, Aaron Boakye, Michael Laryea, Edward Ntim Gasu, Lawrence Sheringham Borquaye","doi":"10.1080/07391102.2023.2292297","DOIUrl":"https://doi.org/10.1080/07391102.2023.2292297","url":null,"abstract":"Antimicrobial resistance is a pressing global health concern, underscoring the need for alternative treatments. Antimicrobial peptides (AMPs) have shown promise in this regard, with maximin 1 being...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"117 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138680686","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}
In recent years, exploring the potential of miRNAs as novel diagnostic, prognostic and diagnostic markers have gained much attention. In current study, we conducted an in-depth circRNA-miRNA-mRNA i...
{"title":"CircRNA-miRNA-mRNA interactome analysis in endometrial cancer","authors":"Tikam Chand Dakal, Abhishek Kumar, Pawan Kumar Maurya","doi":"10.1080/07391102.2023.2291834","DOIUrl":"https://doi.org/10.1080/07391102.2023.2291834","url":null,"abstract":"In recent years, exploring the potential of miRNAs as novel diagnostic, prognostic and diagnostic markers have gained much attention. In current study, we conducted an in-depth circRNA-miRNA-mRNA i...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138680691","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2291544
Xianyang Zeng, Risong Na, Lianjuan Yang, Xi Zhao, Xuri Huang
Proton-dependent glucose transporters as important drug targets can have different protonation states and adjust their conformational state under different pHs. So based on this character, research...
{"title":"Inhibition mechanism understanding from molecular dynamics simulation of the interactions between several flavonoids and proton-dependent glucose transporter","authors":"Xianyang Zeng, Risong Na, Lianjuan Yang, Xi Zhao, Xuri Huang","doi":"10.1080/07391102.2023.2291544","DOIUrl":"https://doi.org/10.1080/07391102.2023.2291544","url":null,"abstract":"Proton-dependent glucose transporters as important drug targets can have different protonation states and adjust their conformational state under different pHs. So based on this character, research...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"286 1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629361","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2292298
Ozge Gungor, Yunus Emre Veziroglu, Aysegul Kose, Seyit Ali Gungor, Muhammet Kose
1,2,3-Triazole compounds (1a–3a) and their oxime derivatives (1b–3b) were synthesized. The structures of these synthesized compounds were characterized using common spectroscopic methods. Crystal s...
{"title":"New 1,2,3-triazoles and their oxime derivatives: AChE/BChE enzyme inhibitory and DNA binding properties","authors":"Ozge Gungor, Yunus Emre Veziroglu, Aysegul Kose, Seyit Ali Gungor, Muhammet Kose","doi":"10.1080/07391102.2023.2292298","DOIUrl":"https://doi.org/10.1080/07391102.2023.2292298","url":null,"abstract":"1,2,3-Triazole compounds (1a–3a) and their oxime derivatives (1b–3b) were synthesized. The structures of these synthesized compounds were characterized using common spectroscopic methods. Crystal s...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"55 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629362","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2291829
Farnaz Palhamkhani, Milad Alipour, Abbas Dehnad, Karim Abbasi, Parvin Razzaghi, Jahan B. Ghasemi
Virtual screening has emerged as a valuable computational tool for predicting compound–protein interactions, offering a cost-effective and rapid approach to identifying potential candidate drug mol...
{"title":"DeepCompoundNet: enhancing compound–protein interaction prediction with multimodal convolutional neural networks","authors":"Farnaz Palhamkhani, Milad Alipour, Abbas Dehnad, Karim Abbasi, Parvin Razzaghi, Jahan B. Ghasemi","doi":"10.1080/07391102.2023.2291829","DOIUrl":"https://doi.org/10.1080/07391102.2023.2291829","url":null,"abstract":"Virtual screening has emerged as a valuable computational tool for predicting compound–protein interactions, offering a cost-effective and rapid approach to identifying potential candidate drug mol...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629083","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2291179
Ghadir A. Jamal, Ehsan Jahangirian, Michael R. Hamblin, Masoud Shirali, Hamed Mirzaei, Hossein Tarrahimofrad
One of the major categories of industrial enzymes, proteases is crucial to the survival of living things. The purpose of this research was to newly thermostable protease from the thermophilum Geoba...
蛋白酶是工业酶的主要种类之一，对生物的生存至关重要。本研究的目的是从嗜热菌中提取新的耐热蛋白酶。
{"title":"In-silico characterization of a thermophilic serine protease via homology modeling, docking and molecular dynamics simulations","authors":"Ghadir A. Jamal, Ehsan Jahangirian, Michael R. Hamblin, Masoud Shirali, Hamed Mirzaei, Hossein Tarrahimofrad","doi":"10.1080/07391102.2023.2291179","DOIUrl":"https://doi.org/10.1080/07391102.2023.2291179","url":null,"abstract":"One of the major categories of industrial enzymes, proteases is crucial to the survival of living things. The purpose of this research was to newly thermostable protease from the thermophilum Geoba...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629348","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2293278
Samia A. Elseginy
The COVID-19 pandemic was caused by the SARS-CoV-2 virus, frequent mutations occurred to the wild-type virus resulting in evolved new variants. The WHO classified the new variants as ‘Variants of C...
{"title":"Exploring binding mechanisms of omicron spike protein with dolutegravir and etravirine by molecular dynamics simulation, principal component analysis, and free binding energy calculations","authors":"Samia A. Elseginy","doi":"10.1080/07391102.2023.2293278","DOIUrl":"https://doi.org/10.1080/07391102.2023.2293278","url":null,"abstract":"The COVID-19 pandemic was caused by the SARS-CoV-2 virus, frequent mutations occurred to the wild-type virus resulting in evolved new variants. The WHO classified the new variants as ‘Variants of C...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"30 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629074","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}
Pub Date : 2023-12-12DOI: 10.1080/07391102.2023.2291830
Sevil Kalin, Ferah Comert Onder
The p90 ribosomal protein S6 Kinase (RSK) family belongs to Ser/Thr protein kinases that includes four isoform RSK1-4 in mammals. The ribosomal protein S6 Kinase 1 (RSK1) is also known as ribosomal...
{"title":"Discovery of potential RSK1 inhibitors for cancer therapy using virtual screening, molecular docking, molecular dynamics simulation, and MM/GBSA calculations","authors":"Sevil Kalin, Ferah Comert Onder","doi":"10.1080/07391102.2023.2291830","DOIUrl":"https://doi.org/10.1080/07391102.2023.2291830","url":null,"abstract":"The p90 ribosomal protein S6 Kinase (RSK) family belongs to Ser/Thr protein kinases that includes four isoform RSK1-4 in mammals. The ribosomal protein S6 Kinase 1 (RSK1) is also known as ribosomal...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"98 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629087","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}
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