Pub Date : 2024-03-20DOI: 10.1080/07391102.2024.2328736
Jad Abbass, Charles Parisi
In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creatio...
{"title":"Machine learning-based prediction of proteins’ architecture using sequences of amino acids and structural alphabets","authors":"Jad Abbass, Charles Parisi","doi":"10.1080/07391102.2024.2328736","DOIUrl":"https://doi.org/10.1080/07391102.2024.2328736","url":null,"abstract":"In addition to the growth of protein structures generated through wet laboratory experiments and deposited in the PDB repository, AlphaFold predictions have significantly contributed to the creatio...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"2014 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140172203","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 : 2024-03-19DOI: 10.1080/07391102.2024.2323702
Ashraf B. Abdel-Naim, Pawan Kumar, Mohammed A. Bazuhair, Waleed Y. Rizg, Hatoon A. Niyazi, Khalil Alkuwaity, Hanouf A. Niyazi, Saif A. Alharthy, Steve Harakeh, Shafiul Haque, Amresh Prakash, Vijay Kumar
The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-termin...
{"title":"Computational insights into dynamics and conformational stability of N-acetylmannosamine kinase mutations","authors":"Ashraf B. Abdel-Naim, Pawan Kumar, Mohammed A. Bazuhair, Waleed Y. Rizg, Hatoon A. Niyazi, Khalil Alkuwaity, Hanouf A. Niyazi, Saif A. Alharthy, Steve Harakeh, Shafiul Haque, Amresh Prakash, Vijay Kumar","doi":"10.1080/07391102.2024.2323702","DOIUrl":"https://doi.org/10.1080/07391102.2024.2323702","url":null,"abstract":"The activity of UDP-GlcNAc 2-epimerase/ManNAc kinase (GNE) is essential for the biosynthesis of sialic acid, which is involved in cellular processes in health and diseases. GNE contains an N-termin...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"21 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140172211","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 : 2024-03-18DOI: 10.1080/07391102.2024.2329304
Melissa Louise Stofberg, Florence Lisa Muzenda, Ikechukwu Achilonu, Erick Strauss, Tawanda Zininga
Plasmodium falciparum parasites export more than 400 proteins to remodel the host cell environment and increase its chances of surviving and reproducing. The endoplasmic reticulum (ER) plays a cent...
{"title":"In silico screening of selective ATP mimicking inhibitors targeting the Plasmodium falciparum Grp94","authors":"Melissa Louise Stofberg, Florence Lisa Muzenda, Ikechukwu Achilonu, Erick Strauss, Tawanda Zininga","doi":"10.1080/07391102.2024.2329304","DOIUrl":"https://doi.org/10.1080/07391102.2024.2329304","url":null,"abstract":"Plasmodium falciparum parasites export more than 400 proteins to remodel the host cell environment and increase its chances of surviving and reproducing. The endoplasmic reticulum (ER) plays a cent...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"69 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140151338","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 : 2024-03-05DOI: 10.1080/07391102.2024.2322639
Gauri Shankar, Yusuf Akhter
Iron acquisition is critical to the virulence of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To acquire iron within the host, Mtb secretes siderophores that chelate iron ...
{"title":"Molecular insights into ferric-siderophore transport by the putative TonB-dependent transporter in Mycobacterium tuberculosis","authors":"Gauri Shankar, Yusuf Akhter","doi":"10.1080/07391102.2024.2322639","DOIUrl":"https://doi.org/10.1080/07391102.2024.2322639","url":null,"abstract":"Iron acquisition is critical to the virulence of Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis. To acquire iron within the host, Mtb secretes siderophores that chelate iron ...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"35 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140070273","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}
Abietatrien-3β-ol (ATO) was isolated from the aerial part of the Nepeta italica subsp. italica methanol-chloroform extract and studied antioxidant, enzyme inhibition, and DNA protection activities....
从Nepeta italica subsp. italica甲醇-氯仿提取物的气生部分分离出Abietatrien-3β-ol（ATO），并对其抗氧化、酶抑制和DNA保护活性进行了研究....。
{"title":"In vitro bioactivities and in silico enzyme interactions of abietatrien-3β-ol by bio-guided isolation from Nepeta italica subsp. italica","authors":"Yaşar İpek, Yunus Başar, Semiha Yenigün, Lütfi Behçet, Tevfik Özen, İbrahim Demirtaş","doi":"10.1080/07391102.2024.2322626","DOIUrl":"https://doi.org/10.1080/07391102.2024.2322626","url":null,"abstract":"Abietatrien-3β-ol (ATO) was isolated from the aerial part of the Nepeta italica subsp. italica methanol-chloroform extract and studied antioxidant, enzyme inhibition, and DNA protection activities....","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140070222","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 : 2024-02-26DOI: 10.1080/07391102.2024.2316767
Abdulfattah Y. Alhazmi, Farhan R. Khan, Zia ur Rehman, Ali Hazazi, Bader S. Alotaibi, Nahed S. Alharthi, Hayaa M. Alhuthali, Faris F. Aba Alkhayl, Faez Falah Alshehri, Abdulaziz Alkhoshaiban, Faisal Al-Otaibi
One of the viral diseases that affect millions of people around the world, particularly in developing countries, is Japanese encephalitis (JE). In this study, the conserved protein of this virus, t...
{"title":"Structural and energetic analysis of NS5 protein inhibition by small molecules in Japanese encephalitis virus using machine learning and steered molecular dynamics approach","authors":"Abdulfattah Y. Alhazmi, Farhan R. Khan, Zia ur Rehman, Ali Hazazi, Bader S. Alotaibi, Nahed S. Alharthi, Hayaa M. Alhuthali, Faris F. Aba Alkhayl, Faez Falah Alshehri, Abdulaziz Alkhoshaiban, Faisal Al-Otaibi","doi":"10.1080/07391102.2024.2316767","DOIUrl":"https://doi.org/10.1080/07391102.2024.2316767","url":null,"abstract":"One of the viral diseases that affect millions of people around the world, particularly in developing countries, is Japanese encephalitis (JE). In this study, the conserved protein of this virus, t...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139968963","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 : 2024-02-26DOI: 10.1080/07391102.2024.2316762
Israr Fatima, Fahad M. Alshabrmi, Tariq Aziz, Abdulhakeem S. Alamri, Majid Alhomrani, Saad Alghamdi, Reem Ahmad Alghuraybi, Ahmad O. Babalghith, Ghazi A. Bamagous, Zain Alhindi, Anas S. Dablool, Areej A. Alhhazmi, Mashael W. Alruways
Citrobacter koseri is a gram-negative rod that has been linked to infections in people with significant comorbidities and immunocompromised immune systems. It is most commonly known to cause urinar...
{"title":"Revolutionizing and identifying novel drug targets in Citrobacter koseri via subtractive proteomics and development of a multi-epitope vaccine using reverse vaccinology and immuno-informatics","authors":"Israr Fatima, Fahad M. Alshabrmi, Tariq Aziz, Abdulhakeem S. Alamri, Majid Alhomrani, Saad Alghamdi, Reem Ahmad Alghuraybi, Ahmad O. Babalghith, Ghazi A. Bamagous, Zain Alhindi, Anas S. Dablool, Areej A. Alhhazmi, Mashael W. Alruways","doi":"10.1080/07391102.2024.2316762","DOIUrl":"https://doi.org/10.1080/07391102.2024.2316762","url":null,"abstract":"Citrobacter koseri is a gram-negative rod that has been linked to infections in people with significant comorbidities and immunocompromised immune systems. It is most commonly known to cause urinar...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139969296","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}
The Unfolded protein response (UPR) is an adaptive signalling pathway which is triggered by accumulation of unfolded/misfolded protein in ER lumen. The UPR consist of three transmembrane proteins-I...
{"title":"Elucidating the EXOSC3-IRE1α interaction: a convergent study incorporating computational, in vitro and in vivo studies","authors":"Ariha Ashraf, Younis Majeed, Irfan Gul, Mariam Banday, Khalida Ramzan, Khalid Majid Fazili","doi":"10.1080/07391102.2024.2320252","DOIUrl":"https://doi.org/10.1080/07391102.2024.2320252","url":null,"abstract":"The Unfolded protein response (UPR) is an adaptive signalling pathway which is triggered by accumulation of unfolded/misfolded protein in ER lumen. The UPR consist of three transmembrane proteins-I...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139969424","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}
The current trend in biomedical research is on prioritizing infections based on multidrug resistance. Elizabethkingia meningoseptica, a nosocomial infection-causing organism emerging from Neonatal ...
{"title":"Insilico screening to identify novel inhibitors targeting 30S ribosomal protein S12 in meningitis-causing organism ‘Elizabethkingia meningoseptica’","authors":"Neha Girdhar, Vikas Yadav, Nilima Kumari, Naidu Subbarao, Annangarachari Krishnamachari","doi":"10.1080/07391102.2024.2321511","DOIUrl":"https://doi.org/10.1080/07391102.2024.2321511","url":null,"abstract":"The current trend in biomedical research is on prioritizing infections based on multidrug resistance. Elizabethkingia meningoseptica, a nosocomial infection-causing organism emerging from Neonatal ...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"78 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139969536","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}
Oral cancer is a widespread health concern in rural India due to a lack of awareness, delayed diagnosis and limited access to affordable treatment options. The current chemotherapy has notable side...
{"title":"Network pharmacology integrated molecular docking of fucoidan against oral cancer and in vitro evaluation- A study using GEO datasets","authors":"Arul Jayanthi Antonisamy, Karthikeyan Rajendran, Premnath Dhanaraj","doi":"10.1080/07391102.2024.2316771","DOIUrl":"https://doi.org/10.1080/07391102.2024.2316771","url":null,"abstract":"Oral cancer is a widespread health concern in rural India due to a lack of awareness, delayed diagnosis and limited access to affordable treatment options. The current chemotherapy has notable side...","PeriodicalId":15085,"journal":{"name":"Journal of Biomolecular Structure and Dynamics","volume":"37 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139921738","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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