Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 4 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 4 (2023)

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Research Articles

Article
In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks
Wan-Atirah Azemin, Nadiawati Alias, Abdul Manaf Ali & Mohd Shahir Shamsir
Pages: 1141-1167
Published online: 22 Dec 2021
AbstractforIn silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks | Full Text | References | PDF (5.5 MB) | EPUB
  • 329 Views
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Article
DFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins
Yousif Taha Hussein & Yousif Hussein Azeez
Pages: 1168-1177
Published online: 21 Dec 2021
AbstractforDFT analysis and in silico exploration of drug-likeness, toxicity prediction, bioactivity score, and chemical reactivity properties of the urolithins | Full Text | References | PDF (1.7 MB) | EPUB
  • 484 Views
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Article
Elucidation of kinetic and structural properties of eye lens ζ-crystallin: an in vitro and in silico approach
Md Amiruddin Hashmi, Ajamaluddin Malik, Abdullah Arsalan, Masood Alam Khan & Hina Younus
Pages: 1178-1192
Published online: 20 Dec 2021
AbstractforElucidation of kinetic and structural properties of eye lens ζ-crystallin: an in vitro and in silico approach | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 219 Views
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Article
Protein–protein docking and molecular dynamics studies of sericin and cocoonase of silkworm: an insight for cocoon softening
Nishi Prakash Tiwari, Jay Prakash Pandey & Dev Mani Pandey
Pages: 1193-1205
Published online: 23 Dec 2021
AbstractforProtein–protein docking and molecular dynamics studies of sericin and cocoonase of silkworm: an insight for cocoon softening | Full Text | References | PDF (5.5 MB) | EPUB
  • 584 Views
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Article
Antioxidant and anticholinesterase activities of amentoflavone isolated from Ouratea fieldingiana (Gardner) Engl. through in vitro and chemical-quantum studies
Lucas Soares Frota, Daniela Ribeiro Alves, Márcia Machado Marinho, Leonardo Paes da Silva, Francisco Wagner de Queiroz Almeida Neto, Emmanuel Silva Marinho & Selene Maia de Morais
Pages: 1206-1216
Published online: 15 Dec 2021
AbstractforAntioxidant and anticholinesterase activities of amentoflavone isolated from Ouratea fieldingiana (Gardner) Engl. through in vitro and chemical-quantum studies | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 220 Views
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Article
Characterization of SARS-CoV-2 isolated from a patient in Iran compared to SARS-CoV-2 different variants
Khadijeh Ahmadi, Mahmood Hosseinpour, Elham Rismani, Mehdi Hassaniazad, Ladan Mafakher, Hamid Reza Jahantigh, Ebrahim Eftekhar & Hamed Gouklani
Pages: 1217-1232
Published online: 10 Jan 2022
AbstractforCharacterization of SARS-CoV-2 isolated from a patient in Iran compared to SARS-CoV-2 different variants | Full Text | References | PDF (4.9 MB) | EPUB
  • 120 Views
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Article
Design, synthesis, biomedical investigation, DFT calculation and molecular docking of novel Ru(II)-mixed ligand complexes
Sara E. Mohamed, Ramadan M. Ramadan, Amir E. Aboelhasan & Ayman A. Abdel Aziz
Pages: 1233-1252
Published online: 20 Dec 2021
AbstractforDesign, synthesis, biomedical investigation, DFT calculation and molecular docking of novel Ru(II)-mixed ligand complexes | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 183 Views
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Article
Structure assignment, conformational properties and discovery of potential targets of the Ugi cinnamic adduct NGI25
Nikitas Georgiou, Niki Gouleni, Eleni Chontzopoulou, George S. Skoufas, Anastasios Gkionis, Demeter Tzeli, Stamatia Vassiliou & Thomas Mavromoustakos
Pages: 1253-1266
Published online: 29 Dec 2021
AbstractforStructure assignment, conformational properties and discovery of potential targets of the Ugi cinnamic adduct NGI25 | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 165 Views
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Article
Discovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling
Bipasa Kar, Chanakya Nath Kundu, Sanghamitra Pati & Debdutta Bhattacharya
Pages: 1267-1280
Published online: 28 Dec 2021
AbstractforDiscovery of phyto-compounds as novel inhibitors against NDM-1 and VIM-1 protein through virtual screening and molecular modelling | Full Text | References | PDF (3 MB) | EPUB
  • 339 Views
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Article
Interactions between phenolic constituents of Scutellaria salviifolia and key targets associated with inflammation: network pharmacology, molecular docking analysis and in vitro assays
Zeynep Dogan, Vahap Murat Kutluay, Yasin Genc & Iclal Saracoglu
Pages: 1281-1294
Published online: 23 Dec 2021
AbstractforInteractions between phenolic constituents of Scutellaria salviifolia and key targets associated with inflammation: network pharmacology, molecular docking analysis and in vitro assays | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 459 Views
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Article
Genome-wide identification and analysis of the PAL genes from the orchids Apostasia shenzhenica, Dendrobium catenatum and Phalaenopsis equestris
Santosh Kumar Vishwakarma, Nutan Singh & Suman Kumaria
Pages: 1295-1308
Published online: 29 Dec 2021
AbstractforGenome-wide identification and analysis of the PAL genes from the orchids Apostasia shenzhenica, Dendrobium catenatum and Phalaenopsis equestris | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 446 Views
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Article
DNA-binding, cleavage, antibacterial and in vitro anticancer activity of copper(II) mixed ligand complexes of 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino)aceticacid and polypyridyl ligands
Thatituri Sabithakala & Chittireddy Venkata Ramana Reddy
Pages: 1309-1321
Published online: 29 Dec 2021
AbstractforDNA-binding, cleavage, antibacterial and in vitro anticancer activity of copper(II) mixed ligand complexes of 2-(((6-chloro-1H-benzo[d]imidazol-2-yl)methyl)amino)aceticacid and polypyridyl ligands | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 169 Views
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Article
Multifaceted 3D-QSAR analysis for the identification of pharmacophoric features of biphenyl analogues as aromatase inhibitors
Laxmi Banjare, Yogesh Singh, Sant Kumar Verma, Atul Kumar Singh, Pradeep Kumar, Shashank Kumar, Akhlesh Kumar Jain & Suresh Thareja
Pages: 1322-1341
Published online: 29 Dec 2021
AbstractforMultifaceted 3D-QSAR analysis for the identification of pharmacophoric features of biphenyl analogues as aromatase inhibitors | Full Text | References | PDF (4.8 MB) | EPUB
  • 197 Views
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Article
Molecular docking and dynamic simulation analysis of Hepatitis E virus protease in complexing with the E64 inhibitor
Meenakshi Chaudhary, Vikrant Nain & Deepak Sehgal
Pages: 1342-1350
Published online: 21 Dec 2021
AbstractforMolecular docking and dynamic simulation analysis of Hepatitis E virus protease in complexing with the E64 inhibitor | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 199 Views
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Article
Investigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis
Jaganathan Ramakrishnan, Sivanandam Magudeeswaran, Suganya Suresh & Kumaradhas Poomani
Pages: 1351-1365
Published online: 03 Jan 2022
AbstractforInvestigation of intermolecular interactions and binding mechanism of PU139 and PU141 molecules with p300 HAT enzyme via molecular docking, molecular dynamics simulations and binding free energy analysis | Full Text | References | PDF (4.1 MB) | EPUB
  • 202 Views
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Article
A quinoline alkaloid potentially modulates the amyloidogenic structural transitions of the biofilm scaffolding small basic protein
Nikita Admane, Ram Kothandan, Sowfia Syed & Sumit Biswas
Pages: 1366-1377
Published online: 29 Dec 2021
AbstractforA quinoline alkaloid potentially modulates the amyloidogenic structural transitions of the biofilm scaffolding small basic protein | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 155 Views
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Article
Biomolecular interactions and binding dynamics of inhibitor arachidonic acid, with tyrosinase enzyme
Tahereh Shojazadeh, Leila Zolghadr, Saeed JafarKhani, Sajjad Gharaghani, Alireza Farasat, Hossein Piri & Nematollah Gheibi
Pages: 1378-1387
Published online: 03 Jan 2022
AbstractforBiomolecular interactions and binding dynamics of inhibitor arachidonic acid, with tyrosinase enzyme | Full Text | References | PDF (1.7 MB) | EPUB
  • 208 Views
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Article
Characterization and tissue expression analysis of mitochondrial creatine kinases (types I and II) from Pelodiscus sinensis
Li-Fang Zeng, Jinhyuk Lee, Gyutae Lim, Yu-Fei Yang, Run-Lan Lin, Shang-Jun Yin, Wei Wang & Yong-Doo Park
Pages: 1388-1402
Published online: 23 Dec 2021
AbstractforCharacterization and tissue expression analysis of mitochondrial creatine kinases (types I and II) from Pelodiscus sinensis | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 154 Views
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Article
Phytochemical rich Himalayan Rhododendron arboreum petals inhibit SARS-CoV-2 infection in vitro
Maneesh Lingwan, Shagun Shagun, Falak Pahwa, Ankit Kumar, Dileep Kumar Verma, Yogesh Pant, Lingarao V. K. Kamatam, Bandna Kumari, Ranjan Kumar Nanda, Sujatha Sunil & Shyam Kumar Masakapalli
Pages: 1403-1413
Published online: 28 Dec 2021
AbstractforPhytochemical rich Himalayan Rhododendron arboreum petals inhibit SARS-CoV-2 infection in vitro | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 1053 Views
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Article
Modeling, molecular dynamics and docking studies of a full-length Echinococcus granulosus 2DBD nuclear receptor
Saira Cancela, Adriana Esteves, Gabriela Alvite & Margot Paulino
Pages: 1414-1423
Published online: 07 Jan 2022
AbstractforModeling, molecular dynamics and docking studies of a full-length Echinococcus granulosus 2DBD nuclear receptor | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 218 Views
  • 1 CrossRef citations
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Article
Isolation, characterisation, anticancer and anti-oxidant activities of 2-methoxy mucic acid from Rhizophora apiculata: an in vitro and in silico studies
A. Parthiban, V. Sachithanandam, P. Lalitha, Jayaraman Muthukumaran, Ranjita Misra, Monika Jain, R. Sridhar, T. Mageswaran, Ramachandran Purvaja & Ramachandran Ramesh
Pages: 1424-1436
Published online: 29 Dec 2021
AbstractforIsolation, characterisation, anticancer and anti-oxidant activities of 2-methoxy mucic acid from Rhizophora apiculata: an in vitro and in silico studies | Full Text | References | PDF (3.6 MB) | EPUB
  • 191 Views
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Article
What make malarial adenosine deaminase from PLASMODIUM VIVAX recognise adenosine and 5′-methylthioadenosine: simulation studies
Warot Chotpatiwetchkul, Sirin Sittiwanichai, Jitti Niramitranon & Prapasiri Pongprayoon
Pages: 1437-1444
Published online: 07 Jan 2022
AbstractforWhat make malarial adenosine deaminase from PLASMODIUM VIVAX recognise adenosine and 5′-methylthioadenosine: simulation studies | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 227 Views
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Article
Evolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of ‘peptidase’ domain of Spt16
Neeraj K. Gaur, Biplab Ghosh, Venuka Durani Goyal, Kiran Kulkarni & Ravindra D. Makde
Pages: 1445-1457
Published online: 31 Dec 2021
AbstractforEvolutionary conservation of protein dynamics: insights from all-atom molecular dynamics simulations of ‘peptidase’ domain of Spt16 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 245 Views
  • 1 CrossRef citations
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Article
Computational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene
Soumalya Sarkar, Vivek K. Gupta, Samridhi Sharma, Ting Shen, Veer Gupta, Mehdi Mirzaei, Stuart L. Graham & Nitin Chitranshi
Pages: 1458-1478
Published online: 31 Dec 2021
AbstractforComputational refinement identifies functional destructive single nucleotide polymorphisms associated with human retinoid X receptor gene | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 500 Views
  • 3 CrossRef citations
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Article
Serine 106 preserves the tertiary structure, function, and stability of a cyclophilin from Staphylococcus aureus
Soham Seal, Nilanjan Banerjee, Rohit Mahato, Tanmoy Kundu, Debabrata Sinha, Tushar Chakraborty, Debasmita Sinha, Keya Sau, Subhrangsu Chatterjee & Subrata Sau
Pages: 1479-1494
Published online: 30 Dec 2021
AbstractforSerine 106 preserves the tertiary structure, function, and stability of a cyclophilin from Staphylococcus aureus | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 149 Views
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Article
Molecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12
Shruti Gupta & Shamsher Singh Kanwar
Pages: 1495-1509
Published online: 10 Jan 2022
AbstractforMolecular characterization and in silico analysis of oxalate decarboxylase of Pseudomonas sp. OXDC12 | Full Text | References | PDF (2.9 MB) | EPUB
  • 212 Views
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Article
Molecular docking, pharmacophore modelling, MD simulation and in silico ADMET study reveals bitter cola constituents as potential inhibitors of SARS-CoV-2 main protease and RNA dependent-RNA polymerase
Abimbola Peter Oluyori, Bolatito Eunice Olanipekun, Oluyomi Stephen Adeyemi, Godshelp Osas Egharevba, Abayomi Emmanuel Adegboyega & Oluwole Solomon Oladeji
Pages: 1510-1525
Published online: 07 Jan 2022
AbstractforMolecular docking, pharmacophore modelling, MD simulation and in silico ADMET study reveals bitter cola constituents as potential inhibitors of SARS-CoV-2 main protease and RNA dependent-RNA polymerase | Full Text | References | PDF (5.1 MB) | EPUB
  • 428 Views
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