Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 7 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 7 (2021)

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Research Articles

Article
Computational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy
Priya Kumari & Raju Poddar
Pages: 2289-2301
Published online: 10 Apr 2020
AbstractforComputational modeling for mutational analysis of nitrilase enzyme towards enhancement of binding empathy | Full Text | References | PDF (4.4 MB) | EPUB
  • 243 Views
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Article
E-pharmacophore based virtual screening for identification of dual specific PDE5A and PDE3A inhibitors as potential leads against cardiovascular diseases
Arooma Maryam, Rana Rehan Khalid, Abdul Rauf Siddiqi & Abdulilah Ece
Pages: 2302-2317
Published online: 17 Apr 2020
AbstractforE-pharmacophore based virtual screening for identification of dual specific PDE5A and PDE3A inhibitors as potential leads against cardiovascular diseases | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 452 Views
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Article
Comprehensive investigation of selectivity landscape of glycogen synthase kinase-3 inhibitors
Liliana Pacureanu, Sorin Avram & Luminita Crisan
Pages: 2318-2337
Published online: 07 Apr 2020
AbstractforComprehensive investigation of selectivity landscape of glycogen synthase kinase-3 inhibitors | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 104 Views
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Article
Structure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation
Shiv Bharadwaj, Akhilesh Kumar Rao, Vivek Dhar Dwivedi, Sarad Kumar Mishra & Umesh Yadava
Pages: 2338-2351
Published online: 07 Apr 2020
AbstractforStructure-based screening and validation of bioactive compounds as Zika virus methyltransferase (MTase) inhibitors through first-principle density functional theory, classical molecular simulation and QM/MM affinity estimation | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 575 Views
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Article
An effective molecular blocker of ion channel of M2 protein as anti-influenza a drug
Yury N. Vorobjev
Pages: 2352-2363
Published online: 09 Apr 2020
AbstractforAn effective molecular blocker of ion channel of M2 protein as anti-influenza a drug | Full Text | References | PDF (2.4 MB) | EPUB
  • 272 Views
  • 3 CrossRef citations
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Article
Structural disorder originates beyond narrow stoichiometric margins of amino acids in naturally occurring folded proteins
Aditya Mittal, Anandkumar Madhavjibhai Changani, Sakshi Taparia, Deepanshu Goel, Animesh Parihar & Ishan Singh
Pages: 2364-2375
Published online: 20 Apr 2020
AbstractforStructural disorder originates beyond narrow stoichiometric margins of amino acids in naturally occurring folded proteins | Full Text | References | PDF (2.1 MB) | EPUB
  • 417 Views
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Article
Synthesis, antimicrobial activity, molecular docking and ADMET study of a caprolactam-glycine cluster
Sefa Celik, Ali Tugrul Albayrak, Sevim Akyuz, Aysen E. Ozel & Belgi Diren Sigirci
Pages: 2376-2386
Published online: 07 Apr 2020
AbstractforSynthesis, antimicrobial activity, molecular docking and ADMET study of a caprolactam-glycine cluster | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 474 Views
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Article
Comprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species
Yasmin Begum & Sunil Kanti Mondal
Pages: 2387-2414
Published online: 15 Apr 2020
AbstractforComprehensive study of the genes involved in chlorophyll synthesis and degradation pathways in some monocot and dicot plant species | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 411 Views
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Article
On the dynamics of a curved microtubule-associated proteins by considering viscoelastic properties of the living biological cells
Zahra Abdelmalek, Mohammed Karbon, Arameh Eyvazian, Ali Forooghi, Hamed Safarpour & Iskander Tlili
Pages: 2415-2429
Published online: 20 Apr 2020
AbstractforOn the dynamics of a curved microtubule-associated proteins by considering viscoelastic properties of the living biological cells | Full Text | References | PDF (2.1 MB) | EPUB
  • 237 Views
  • 15 CrossRef citations
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Article
Anti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: design, synthesis, docking, TOPKAT analysis and molecular dynamics simulations
Vishal K. Singh, Ritika Srivastava, Parth Sarthi Sen Gupta, Farha Naaz, Himani Chaurasia, Richa Mishra, Malay Kumar Rana & Ramendra K. Singh
Pages: 2430-2446
Published online: 11 Apr 2020
AbstractforAnti-HIV potential of diarylpyrimidine derivatives as non-nucleoside reverse transcriptase inhibitors: design, synthesis, docking, TOPKAT analysis and molecular dynamics simulations | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 424 Views
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Article
HIV long-term non-progressors share similar features with simian immunodeficiency virus infection of chimpanzees
Ayan Roy & Surajit Basak
Pages: 2447-2454
Published online: 07 Apr 2020
AbstractforHIV long-term non-progressors share similar features with simian immunodeficiency virus infection of chimpanzees | Full Text | References | PDF (1 MB) | EPUB | Supplemental
  • 126 Views
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Article
Virtual screening by 2-D fingerprints, shape and docking for discovering new chemotypes of activator protein-1 inhibitors
Zhou Yin
Pages: 2455-2462
Published online: 07 Apr 2020
AbstractforVirtual screening by 2-D fingerprints, shape and docking for discovering new chemotypes of activator protein-1 inhibitors | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 162 Views
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Article
Computational elucidation and validation of the three-dimensional structure of humanized aldolase catalytic antibody 38C2
Ranga Srinath Jayakody, Lakshitha Ishara Jasin Arachchige & Achini Japahuge
Pages: 2463-2477
Published online: 20 Apr 2020
AbstractforComputational elucidation and validation of the three-dimensional structure of humanized aldolase catalytic antibody 38C2 | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 381 Views
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Article
Synthesis, biological activity, molecular docking studies of a novel series of 3-Aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives as the acetylcholinesterase inhibitors
Zhe Jin, Chao Zhang, Miao Liu, Simeng Jiao, Jing Zhao, Xiaoping Liu, Huangquan Lin, David Chi-cheong Wan & Chun Hu
Pages: 2478-2489
Published online: 16 Apr 2020
AbstractforSynthesis, biological activity, molecular docking studies of a novel series of 3-Aryl-7H-thiazolo[3,2-b]-1,2,4-triazin-7-one derivatives as the acetylcholinesterase inhibitors | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 212 Views
  • 1 CrossRef citations
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Article
Phenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators
Ilaria Camponeschi, Achille Damasco, Vladimir N. Uversky, Alessandro Giuliani & Michele M. Bianchi
Pages: 2490-2501
Published online: 13 Apr 2020
AbstractforPhenotypic suppression caused by resonance with light-dark cycles indicates the presence of a 24-hours oscillator in yeast and suggests a new role of intrinsically disordered protein regions as internal mediators | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 173 Views
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Article
Structural dynamics and susceptibility of anti-HIV drugs against HBV reverse transcriptase
Jirayu Kammarabutr, Panupong Mahalapbutr, Hisashi Okumura, Peter Wolschann & Thanyada Rungrotmongkol
Pages: 2502-2511
Published online: 20 Apr 2020
AbstractforStructural dynamics and susceptibility of anti-HIV drugs against HBV reverse transcriptase | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 406 Views
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Article
Discovery of small molecule inhibitors through pharmacophore modeling, molecular docking, molecular dynamics simulation and experimental validation against myeloid cell leukemia-1 (Mcl-1)
Muhammad R. Suleiman, Hanxun Wang, Danxia Huang, Huibin Wang, Johnson Joseph, Tianci Huang, Fengjiao Zhang, Jian Wang & Maosheng Cheng
Pages: 2512-2525
Published online: 20 Apr 2020
AbstractforDiscovery of small molecule inhibitors through pharmacophore modeling, molecular docking, molecular dynamics simulation and experimental validation against myeloid cell leukemia-1 (Mcl-1) | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 411 Views
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Article
In silico study of the association of the HLA-A*31:01 allele (human leucocyte antigen allele 31:01) with neuroantigenic epitopes of PLP (proteolipid protein), MBP (myelin basic protein) and MOG proteins (myelin oligodendrocyte glycoprotein) for studying the multiple sclerosis disease pathogenesis
Fatemeh Mohammadi-Milasi, Karim Mahnam & Mostafa Shakhsi-Niaei
Pages: 2526-2542
Published online: 13 Apr 2020
AbstractforIn silico study of the association of the HLA-A*31:01 allele (human leucocyte antigen allele 31:01) with neuroantigenic epitopes of PLP (proteolipid protein), MBP (myelin basic protein) and MOG proteins (myelin oligodendrocyte glycoprotein) for studying the multiple sclerosis disease pathogenesis | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 344 Views
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Article
Dynamic instability responses of the substructure living biological cells in the cytoplasm environment using stress-strain size-dependent theory
Neda Najaafi, Mansoureh Jamali, Mostafa Habibi, Seyedehfatemeh Sadeghi, Dong won Jung & Narjes Nabipour
Pages: 2543-2554
Published online: 17 Apr 2020
AbstractforDynamic instability responses of the substructure living biological cells in the cytoplasm environment using stress-strain size-dependent theory | Full Text | References | PDF (2.1 MB) | EPUB
  • 247 Views
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Article
RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions
Mengisteab Gebrezgiabher, Waleed A. Zalloum, David J. Clarke, Steven M. Miles, Antonina A. Fedorova, Marina A. Zenkova & Elena V. Bichenkova
Pages: 2555-2574
Published online: 16 Apr 2020
AbstractforRNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 1366 Views
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Open Access
Article
Understanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation
Dhanawantari L. Singha, Jitendra Maharana, Debashis Panda, Budheswar Dehury, Mahendra Kumar Modi & Salvinder Singh
Pages: 2575-2584
Published online: 05 May 2020
AbstractforUnderstanding the thermal response of rice eukaryotic transcription factor eIF4A1 towards dynamic temperature stress: insights from expression profiling and molecular dynamics simulation | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 290 Views
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Article
Molecular dynamics simulation and binding free energy calculations of microcin J25 binding to the FhuA receptor
Zhenhua Li, Sathishkumar Chinnasamy, Yonghong Zhang & Dong-Qing Wei
Pages: 2585-2594
Published online: 27 Apr 2020
AbstractforMolecular dynamics simulation and binding free energy calculations of microcin J25 binding to the FhuA receptor | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 270 Views
  • 5 CrossRef citations
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Article
Nanoporous iron oxide nanoparticle: hydrothermal fabrication, human serum albumin interaction and potential antibacterial effects
Masoumeh Mehrabi, Mohammad Faezi Ghasemi, Behnam Rasti, Mojtaba Falahati, Amir Mirzaie & Anwarul Hasan
Pages: 2595-2606
Published online: 15 Apr 2020
AbstractforNanoporous iron oxide nanoparticle: hydrothermal fabrication, human serum albumin interaction and potential antibacterial effects | Full Text | References | PDF (3.4 MB) | EPUB
  • 362 Views
  • 10 CrossRef citations
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Article
Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach
Salman Ali Khan, Komal Zia, Sajda Ashraf, Reaz Uddin & Zaheer Ul-Haq
Pages: 2607-2616
Published online: 13 Apr 2020
AbstractforIdentification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach | Full Text | References | PDF (2.2 MB) | EPUB
  • 14213 Views
  • 131 CrossRef citations
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Article
In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel
Manoj Kumar Gupta, Sarojamma Vemula, Ravindra Donde, Gayatri Gouda, Lambodar Behera & Ramakrishna Vadde
Pages: 2617-2627
Published online: 15 Apr 2020
AbstractforIn-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 12199 Views
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Article
Molecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation
Aina Hazimah Bahaman, Roswanira Abdul Wahab, Azzmer Azzar Abdul Hamid, Khairul Bariyyah Abd Halim & Yilmaz Kaya
Pages: 2628-2641
Published online: 20 Apr 2020
AbstractforMolecular docking and molecular dynamics simulations studies on β-glucosidase and xylanase Trichoderma asperellum to predict degradation order of cellulosic components in oil palm leaves for nanocellulose preparation | Full Text | References | PDF (4.1 MB) | EPUB
  • 934 Views
  • 17 CrossRef citations
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Article
Charting the structural and thermodynamic determinants in phenolic acid natural product – cyclodextrin encapsulations
Ioannis Andreadelis, Μaria V. Chatziathanasiadou, Dimitrios Ntountaniotis, Georgia Valsami, Christina Papaemmanouil, Eirini Christodoulou, Gregoria Mitropoulou, Yiannis Kourkoutas, Andreas G. Tzakos & Thomas Mavromoustakos
Pages: 2642-2658
Published online: 16 Apr 2020
AbstractforCharting the structural and thermodynamic determinants in phenolic acid natural product – cyclodextrin encapsulations | Full Text | References | PDF (4.2 MB) | EPUB
  • 274 Views
  • 8 CrossRef citations
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Express Communication

Article
Understanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures
Durgesh Kumar, Kamlesh Kumari, Abhilash Jayaraj, Vinod Kumar, Ramappa Venkatesh Kumar, Sujata K. Dass, Ramesh Chandra & Prashant Singh
Pages: 2659-2672
Published online: 04 May 2020
AbstractforUnderstanding the binding affinity of noscapines with protease of SARS-CoV-2 for COVID-19 using MD simulations at different temperatures | Full Text | References | PDF (3.1 MB) | EPUB
  • 4893 Views
  • 38 CrossRef citations
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Letter to the Editor

Letter
Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19
Nisha Muralidharan, R. Sakthivel, D. Velmurugan & M. Michael Gromiha
Pages: 2673-2678
Published online: 16 Apr 2020
First Page PreviewforComputational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19 | Full Text | References | PDF (1.2 MB) | EPUB
  • 11720 Views
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