Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 11 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 11 (2021)

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Research Articles

Article
Monomeric human soluble CD4 dimerizes at physiological temperature: VTSAXS data based modeling and screening of retardant molecules
Kanika Dhiman, Samir Kumar Nath & Ashish
Pages: 3813-3824
Published online: 01 Jun 2020
AbstractforMonomeric human soluble CD4 dimerizes at physiological temperature: VTSAXS data based modeling and screening of retardant molecules | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 136 Views
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Article
Multi-target approach for Alzheimer’s disease treatment: computational biomolecular modeling of cholinesterase enzymes with a novel 4-N-phenylaminoquinoline derivative reveal promising potentials
Fatima Y. Adeowo, Murtala A. Ejalonibu, Ahmed A. Elrashedy, Monsurat M. Lawal & Hezekiel M. Kumalo
Pages: 3825-3841
Published online: 08 Oct 2020
AbstractforMulti-target approach for Alzheimer’s disease treatment: computational biomolecular modeling of cholinesterase enzymes with a novel 4-N-phenylaminoquinoline derivative reveal promising potentials | Full Text | References | PDF (3.5 MB) | EPUB
  • 258 Views
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Article
Withanone and caffeic acid phenethyl ester are predicted to interact with main protease (Mpro) of SARS-CoV-2 and inhibit its activity
Vipul Kumar, Jaspreet Kaur Dhanjal, Sunil C. Kaul, Renu Wadhwa & Durai Sundar
Pages: 3842-3854
Published online: 01 Jun 2020
AbstractforWithanone and caffeic acid phenethyl ester are predicted to interact with main protease (Mpro) of SARS-CoV-2 and inhibit its activity | Full Text | References | PDF (2.7 MB) | EPUB
  • 7122 Views
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Article
Cytotoxic activity, molecular docking, pharmacokinetic properties and quantum mechanics calculations of the brown macroalga Cystoseira trinodis compounds
Shimaa A. Ahmed, Aziz A. Rahman, Khaled N. M. Elsayed, H. R. Abd El-Mageed, Hussein S. Mohamed & Sayed A. Ahmed
Pages: 3855-3873
Published online: 11 Jun 2020
AbstractforCytotoxic activity, molecular docking, pharmacokinetic properties and quantum mechanics calculations of the brown macroalga Cystoseira trinodis compounds | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 357 Views
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Article
Fluorinated-antioxidant derivatives with improved pharmacological activity: a theoretical study
Yan Zhang, Dongmei Dou & Wei Gu
Pages: 3874-3881
Published online: 04 Jun 2020
AbstractforFluorinated-antioxidant derivatives with improved pharmacological activity: a theoretical study | Full Text | References | PDF (1.4 MB) | EPUB
  • 76 Views
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Article
Targeting the protein-protein interface pocket of Aurora-A-TPX2 complex: rational drug design and validation
Vijay Kumar Bhardwaj & Rituraj Purohit
Pages: 3882-3891
Published online: 08 Jun 2020
AbstractforTargeting the protein-protein interface pocket of Aurora-A-TPX2 complex: rational drug design and validation | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 730 Views
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Article
Molecular insights into the loading and dynamics of anticancer drugs on silicene and folic acid-conjugated silicene nanosheets: DFT calculation and MD simulation
Leila Razavi, Heidar Raissi, Hassan Hashemzadeh & Farzaneh Farzad
Pages: 3892-3899
Published online: 05 Jun 2020
AbstractforMolecular insights into the loading and dynamics of anticancer drugs on silicene and folic acid-conjugated silicene nanosheets: DFT calculation and MD simulation | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 322 Views
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Article
In silico prediction of enzymatic reactions catalyzed by acid phosphatases
Javad Zamani Amirzakaria, Mohammad Ali Malboobi, Sayed-Amir Marashi & Tahmineh Lohrasebi
Pages: 3900-3911
Published online: 02 Jul 2020
AbstractforIn silico prediction of enzymatic reactions catalyzed by acid phosphatases | Full Text | References | PDF (3.2 MB) | EPUB
  • 190 Views
  • 4 CrossRef citations
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Article
Homology modeling, molecular dynamics and virtual screening of endothelin-A receptor for the treatment of pulmonary arterial hypertension
Xi Gu, Ying Wang, Hanxun Wang, Hairui Wu, Wei Li, Jian Wang & Ning Li
Pages: 3912-3923
Published online: 08 Jun 2020
AbstractforHomology modeling, molecular dynamics and virtual screening of endothelin-A receptor for the treatment of pulmonary arterial hypertension | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 375 Views
  • 6 CrossRef citations
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Article
Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening
Osmair Vital de Oliveira, Gerd B. Rocha, Andrew S. Paluch & Luciano T. Costa
Pages: 3924-3933
Published online: 02 Jun 2020
AbstractforRepurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 6162 Views
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Article
Biomolecular interactions and binding dynamics of tyrosine kinase inhibitor erdafitinib, with human serum albumin
Mohd Amir, Mohd Aamir Qureshi & Saleem Javed
Pages: 3934-3947
Published online: 05 Jun 2020
AbstractforBiomolecular interactions and binding dynamics of tyrosine kinase inhibitor erdafitinib, with human serum albumin | Full Text | References | PDF (3.3 MB) | EPUB
  • 396 Views
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Article
Deciphering effectual binding potential of xylo-substrates towards xylose isomerase and xylokinase through molecular docking and molecular dynamic simulation
Sinosh Skariyachan, Ishu Khangwal, Vidya Niranjan, Naveen Kango & Pratyoosh Shukla
Pages: 3948-3957
Published online: 08 Jun 2020
AbstractforDeciphering effectual binding potential of xylo-substrates towards xylose isomerase and xylokinase through molecular docking and molecular dynamic simulation | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 312 Views
  • 3 CrossRef citations
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Article
Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations
Laurence Leherte, Marie Haufroid, Manon Mirgaux & Johan Wouters
Pages: 3958-3974
Published online: 04 Jun 2020
AbstractforInvestigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 131 Views
  • 1 CrossRef citations
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Article
Repurposing of cefpodoxime proxetil as potent neuroprotective agent through computational prediction and in vitro validation
Jishun Quan, Chao Ma, Ying Wang, Baichun Hu, Dongping Zhang, Zhuo Zhang, Jian Wang & Maosheng Cheng
Pages: 3975-3985
Published online: 08 Jun 2020
AbstractforRepurposing of cefpodoxime proxetil as potent neuroprotective agent through computational prediction and in vitro validation | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 135 Views
  • 2 CrossRef citations
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Article
Tracing Brucella evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes
Jian-hua Zhou, Hua Li, Xuerui Li, Jing Gao, Long- Xu, Shengyi Han, Yongsheng Liu, Youjun Shang & Xiaoan Cao
Pages: 3986-3995
Published online: 08 Jun 2020
AbstractforTracing Brucella evolutionary dynamics in expanding host ranges through nucleotide, codon and amino acid usages in genomes | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 159 Views
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Article
Discovery of a new ATP-citrate lyase (ACLY) inhibitor identified by a pharmacophore-based virtual screening study
Vibhu Jha, Salvatore Galati, Valerio Volpi, Lidia Ciccone, Filippo Minutolo, Flavio Rizzolio, Carlotta Granchi, Giulio Poli & Tiziano Tuccinardi
Pages: 3996-4004
Published online: 02 Jun 2020
AbstractforDiscovery of a new ATP-citrate lyase (ACLY) inhibitor identified by a pharmacophore-based virtual screening study | Full Text | References | PDF (2.2 MB) | EPUB
  • 714 Views
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Article
Computational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations
Yeng-Tseng Wang & Tian-Lu Cheng
Pages: 4005-4014
Published online: 08 Jun 2020
AbstractforComputational modeling of cyclic peptide inhibitor–MDM2/MDMX binding through global docking and Gaussian accelerated molecular dynamics simulations | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 488 Views
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Article
Structural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor
Ganesh Kumar Veeramachaneni, V. B. S. C. Thunuguntla, Janakiram Bobbillapati & Jayakumar Singh Bondili
Pages: 4015-4025
Published online: 04 Jun 2020
AbstractforStructural and simulation analysis of hotspot residues interactions of SARS-CoV 2 with human ACE2 receptor | Full Text | References | PDF (3.8 MB) | EPUB
  • 4552 Views
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Article
Quantitative structure–activity relationships of xanthen-3-one and xanthen-1,8-dione derivatives and design of new compounds with enhanced antiproliferative activity on HeLa cervical cancer cells
Selma Zukić, Slavica Oljacic, Katarina Nikolic, Elma Veljović, Selma Špirtović-Halilović, Amar Osmanović & Davorka Završnik
Pages: 4026-4036
Published online: 11 Jun 2020
AbstractforQuantitative structure–activity relationships of xanthen-3-one and xanthen-1,8-dione derivatives and design of new compounds with enhanced antiproliferative activity on HeLa cervical cancer cells | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 355 Views
  • 1 CrossRef citations
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Article
Role of biologically important imidazole moiety on the antimicrobial and anticancer activity of Fe(III) and Mn(II) complexes
M. Shahnawaz Khan, Mohd Umar Hayat, Madiha Khanam, Haris Saeed, Mohammad Owais, Mohd Khalid, M. Shahid & Musheer Ahmad
Pages: 4037-4050
Published online: 25 Jun 2020
AbstractforRole of biologically important imidazole moiety on the antimicrobial and anticancer activity of Fe(III) and Mn(II) complexes | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 391 Views
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Article
Immunoglobulin interface redesigning to enhance lebrikizumab mediated immunomodulation of IL-13 hyper-response
Vinita Sharma, Priya Chouhan, Rajan Kumar Pandey, Rupal Ojha, Veeranarayanan Surya Aathmanathan, Muthukalingan Krishnan & Vijay Kumar Prajapati
Pages: 4051-4065
Published online: 08 Jun 2020
AbstractforImmunoglobulin interface redesigning to enhance lebrikizumab mediated immunomodulation of IL-13 hyper-response | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 199 Views
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Article
Numeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations
Ivan Yu. Torshin, Vladimir A. Namiot, Natalia G. Esipova & Vladimir G. Tumanyan
Pages: 4066-4076
Published online: 11 Jun 2020
AbstractforNumeric analysis of reversibility of classic movement equations and constructive criteria of estimating quality of molecular dynamic simulations | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 78 Views
  • 7 CrossRef citations
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Article
Ruthenium complexes with mono- or bis-heterocyclic chelates: DNA/BSA binding, antioxidant and anticancer studies
Sanam Maikoo, Abir Chakraborty, Nyeleti Vukea, Laura Margaret Kirkpatrick Dingle, William John Samson, Jo-Anne de la Mare, Adrienne Lesley Edkins & Irvin Noel Booysen
Pages: 4077-4088
Published online: 11 Jun 2020
AbstractforRuthenium complexes with mono- or bis-heterocyclic chelates: DNA/BSA binding, antioxidant and anticancer studies | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 715 Views
  • 18 CrossRef citations
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Article
nCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine
Muhammad Hamza, Ashaq Ali, Suliman Khan, Saeed Ahmed, Zarlish Attique, Saad Ur Rehman, Ayesha Khan, Hussain Ali, Muhammad Rizwan, Anum Munir, Arshad Mehmood Khan, Faiza Siddique, Azhar Mehmood, Faisal Nouroz & Sajid Khan
Pages: 4089-4099
Published online: 22 Jun 2020
AbstractfornCOV-19 peptides mass fingerprinting identification, binding, and blocking of inhibitors flavonoids and anthraquinone of Moringa oleifera and hydroxychloroquine | Full Text | References | PDF (2.3 MB) | EPUB
  • 4133 Views
  • 20 CrossRef citations
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Article
Homology modeling of human GABA-AT and devise some novel and potent inhibitors via computer-aided drug design techniques
Anas Al-Obaidi, Ammar D. Elmezayen & Kemal Yelekçi
Pages: 4100-4110
Published online: 08 Jun 2020
AbstractforHomology modeling of human GABA-AT and devise some novel and potent inhibitors via computer-aided drug design techniques | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 464 Views
  • 11 CrossRef citations
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Article
A computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem)
Subhomoi Borkotoky & Manidipa Banerjee
Pages: 4111-4121
Published online: 11 Jun 2020
AbstractforA computational prediction of SARS-CoV-2 structural protein inhibitors from Azadirachta indica (Neem) | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 5342 Views
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Article
Effect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2
Roghayeh Jafarpour, Faezeh Fatemi, Akram Eidi & Faramarz Mehrnejad
Pages: 4122-4132
Published online: 11 Jun 2020
AbstractforEffect of the Met148Leu mutation on the structure and dynamics of the rusticyanin protein from Acidithiobacillus sp. FJ2 | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 156 Views
  • 3 CrossRef citations
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Article
Floral extracts-mediated green synthesis of NiO nanoparticles and their diverse pharmacological evaluations
Ayesha Sani, Dilawar Hassan, Ali Talha Khalil, Affifa Mughal, Ahmed El-Mallul, Muhammad Ayaz, Zhanibek Yessimbekov, Zabta Khan Shinwari & Malik Maaza
Pages: 4133-4147
Published online: 22 Jun 2020
AbstractforFloral extracts-mediated green synthesis of NiO nanoparticles and their diverse pharmacological evaluations | Full Text | References | PDF (3.3 MB) | EPUB
  • 372 Views
  • 19 CrossRef citations
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Article
Structural insights on vitamin D receptor and screening of new potent agonist molecules: structure and ligand-based approach
John Marshal Jayaraj, Everlyne Reteti, Chandrasekhar Kesavan & Karthikeyan Muthusamy
Pages: 4148-4159
Published online: 11 Jun 2020
AbstractforStructural insights on vitamin D receptor and screening of new potent agonist molecules: structure and ligand-based approach | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 243 Views
  • 13 CrossRef citations
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Article
Prunus amygdalus extract exert antidiabetic effect via inhibition of DPP-IV: in-silico and in-vivo approaches
Vikas Kumar, Richa Sachan, Mahfoozur Rahman, Kalicharan Sharma, Fahad A. Al-Abbasi & Firoz Anwar
Pages: 4160-4174
Published online: 30 Jun 2020
AbstractforPrunus amygdalus extract exert antidiabetic effect via inhibition of DPP-IV: in-silico and in-vivo approaches | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 336 Views
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Express Communication

Article
Antiviral effects of probiotic metabolites on COVID-19
Firoz Anwar, Hisham N. Altayb, Fahad A. Al-Abbasi, Abdulrahman L. Al-Malki, Mohammad Amjad Kamal & Vikas Kumar
Pages: 4175-4184
Published online: 09 Jun 2020
AbstractforAntiviral effects of probiotic metabolites on COVID-19 | Full Text | References | PDF (2.8 MB) | EPUB
  • 7441 Views
  • 73 CrossRef citations
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Review Article

Review Article
Covid-19 induced superimposed bacterial infection
Mohamed A. Hendaus & Fatima A. Jomha
Pages: 4185-4191
Published online: 09 Jun 2020
AbstractforCovid-19 induced superimposed bacterial infection | Full Text | References | PDF (1 MB) | EPUB
  • 16109 Views
  • 48 CrossRef citations
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Letters to the editor

Letter
Natural container for drug storage and delivery: chimeric GFP with embedded xenogenic peptide
Ksenia A. Glukhova, Vladislav G. Klyashtorny, Vladimir N. Uversky & Bogdan S. Melnik
Pages: 4192-4197
Published online: 01 Jun 2020
First Page PreviewforNatural container for drug storage and delivery: chimeric GFP with embedded xenogenic peptide | Full Text | References | PDF (1.3 MB) | EPUB
  • 93 Views
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Letter
Synergistic effect of vitamin D and remdesivir can fight COVID-19
Aditya Arya & Vivek Dhar Dwivedi
Pages: 4198-4199
Published online: 09 Jun 2020
CitationforSynergistic effect of vitamin D and remdesivir can fight COVID-19 | Full Text | References | PDF (348.5 KB) | EPUB
  • 1584 Views
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