Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 4 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 4 (2022)

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Research Articles

Article
Unassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation
Brent L. Lee, Krzysztof Kuczera, Kyung-Hoon Lee, Ed W. Childs & Gouri S. Jas
Pages: 1445-1460
Published online: 09 Oct 2020
AbstractforUnassisted N-acetyl-phenylalanine-amide transport across membrane with varying lipid size and composition: kinetic measurements and atomistic molecular dynamics simulation | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
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Article
New insight into the molecular mechanism of the trehalose effect on urate oxidase stability
Zahra Taherimehr, Maryam Zaboli & Masoud Torkzadeh-Mahani
Pages: 1461-1471
Published online: 01 Oct 2020
AbstractforNew insight into the molecular mechanism of the trehalose effect on urate oxidase stability | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 300 Views
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Article
Plant systemic acquired resistance compound salicylic acid as a potent inhibitor against SCF (SKP1-CUL1-F-box protein) mediated complex in Fusarium oxysporum by homology modeling and molecular dynamics simulations
Narendra Kumar Papathoti, Chanon Saengchan, Jayasimha Rayulu Daddam, Nattaya Thongprom, Kodchaphon Tonpho, Toan Le Thanh & Natthiya Buensanteai
Pages: 1472-1479
Published online: 13 Oct 2020
AbstractforPlant systemic acquired resistance compound salicylic acid as a potent inhibitor against SCF (SKP1-CUL1-F-box protein) mediated complex in Fusarium oxysporum by homology modeling and molecular dynamics simulations | Full Text | References | PDF (1.5 MB) | EPUB
  • 343 Views
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Article
Atomistic insight and modeled elucidation of conessine towards Pseudomonas aeruginosa efflux pump
Juntamanee Jewboonchu, Jirakrit Saetang, Dennapa Saeloh, Thanyaluck Siriyong, Thanyada Rungrotmongkol, Supayang Piyawan Voravuthikunchai & Varomyalin Tipmanee
Pages: 1480-1489
Published online: 07 Oct 2020
AbstractforAtomistic insight and modeled elucidation of conessine towards Pseudomonas aeruginosa efflux pump | Full Text | References | PDF (2.3 MB) | EPUB
  • 272 Views
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Article
Biological evaluation of gallic acid and quercetin derived from Ceriops tagal: insights from extensive in vitro and in silico studies
V. Sachithanandam, A. Parthiban, P. Lalitha, Jayaraman Muthukumaran, Monika Jain, Dhanasekar Elumalai, Kamalraja Jayabal, R. Sridhar, Purvaja Ramachandran & Ramesh Ramachandran
Pages: 1490-1502
Published online: 30 Sep 2020
AbstractforBiological evaluation of gallic acid and quercetin derived from Ceriops tagal: insights from extensive in vitro and in silico studies | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 403 Views
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Article
Biochemical investigation of the upstream anti-sickling mechanisms of soursop (Annona muricata): 15-acetyl guanacone as an inhibitor of deoxyhaemoglobin polymerisation
Kingsley Chukwunonso Agu, Merit Ayevbuomwan, Rose Osarieme Imade, Paulinus Ngozi Okolie, Olusola Olalekan Elekofehinti, Abiodun Falodun, Lauretta Nkeiruka Eluehike, Mercy Chinaza Tasie, John Jatto Ovie, Sarah Kelechi Obiajuru, Oghenebrozie Reke Enakeno, Joyce Amiosinor Otsupius, Amina Isimenmen Kashetu & Faith Ofure Akeiti
Pages: 1503-1520
Published online: 05 Oct 2020
AbstractforBiochemical investigation of the upstream anti-sickling mechanisms of soursop (Annona muricata): 15-acetyl guanacone as an inhibitor of deoxyhaemoglobin polymerisation | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
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Article
An in silico approach to identify potential medicinal plants for treating Alzheimer disease: a case study with acetylcholinesterase
Angamba Meetei Potshangbam, Apana Nandeibam, Thongamba Amom, Nongdam Potshangbam, Hamidur Rahaman, Ravindranath Singh Rathore, Laishram Rajendrakumar Singh & Aslam Khan
Pages: 1521-1533
Published online: 06 Oct 2020
AbstractforAn in silico approach to identify potential medicinal plants for treating Alzheimer disease: a case study with acetylcholinesterase | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 475 Views
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Article
Finding potent inhibitors for COVID-19 main protease (Mpro): an in silico approach using SARS-CoV-3CL protease inhibitors for combating CORONA
Mohit Motiwale, Neetu Singh Yadav, Sushil Kumar, Tushar Kushwaha, Gourav Choudhir, Supriya Sharma & Pradeep Kumar Singour
Pages: 1534-1545
Published online: 08 Oct 2020
AbstractforFinding potent inhibitors for COVID-19 main protease (Mpro): an in silico approach using SARS-CoV-3CL protease inhibitors for combating CORONA | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 3156 Views
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Article
In silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2
Mohammed Hakmi, E L Mehdi Bouricha, Jihane Akachar, Badreddine Lmimouni, Jaouad El Harti, Lahcen Belyamani & Azeddine Ibrahimi
Pages: 1546-1557
Published online: 07 Oct 2020
AbstractforIn silico exploration of small-molecule α-helix mimetics as inhibitors of SARS-COV-2 attachment to ACE2 | Full Text | References | PDF (2.7 MB) | EPUB
  • 1589 Views
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Article
Computational studies of the properties and activities of selected trisubstituted benzimidazoles as potential antitubercular drugs inhibiting MTB-FtsZ polymerization
Olayinka I. Akinpelu, Monsurat M. Lawal, Hezekiel M. Kumalo & Ndumiso N. Mhlongo
Pages: 1558-1570
Published online: 06 Oct 2020
AbstractforComputational studies of the properties and activities of selected trisubstituted benzimidazoles as potential antitubercular drugs inhibiting MTB-FtsZ polymerization | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 259 Views
  • 7 CrossRef citations
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Article
Mutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach
Udhaya Kumar. S, Bithia. R, Thirumal Kumar. D, C. George Priya Doss & Hatem Zayed
Pages: 1571-1585
Published online: 09 Oct 2020
AbstractforMutational landscape of K-Ras substitutions at 12th position-a systematic molecular dynamics approach | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 522 Views
  • 15 CrossRef citations
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Article
Using structural analysis to explore the role of hepatitis B virus mutations in immune escape from liver cancer in Chinese, European and American populations
Shuanglin Gu, Li Lv, Xue Lin, Xingyu Li, Juncheng Dai, Jianqiong Zhang, Ren Kong, Wei Xie & Jian Li
Pages: 1586-1596
Published online: 08 Oct 2020
AbstractforUsing structural analysis to explore the role of hepatitis B virus mutations in immune escape from liver cancer in Chinese, European and American populations | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 1637 Views
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Open Access
Article
Molecular dynamics analysis predicts ritonavir and naloxegol strongly block the SARS-CoV-2 spike protein-hACE2 binding
Milad Bagheri & Ahmadreza Niavarani
Pages: 1597-1606
Published online: 08 Oct 2020
AbstractforMolecular dynamics analysis predicts ritonavir and naloxegol strongly block the SARS-CoV-2 spike protein-hACE2 binding | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 2386 Views
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Article
Designed thiazolidines: an arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations
Mahendra Kumar Meena, Durgesh Kumar, Abhilash Jayaraj, Ajay Kumar, Kamlesh Kumari, L. M. Katata-Seru, Indra Bahadur, Vinod Kumar, Anjali Sherawat & Prashant Singh
Pages: 1607-1616
Published online: 19 Oct 2020
AbstractforDesigned thiazolidines: an arsenal for the inhibition of nsP3 of CHIKV using molecular docking and MD simulations | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 295 Views
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Article
Natural bioactive compounds as a new source of promising G protein-coupled estrogen receptor (GPER) modulators: comprehensive in silico approach
Shafi Ullah Khan, Nafees Ahemad, Lay-Hong Chuah, Rakesh Naidu & Thet Thet Htar
Pages: 1617-1628
Published online: 15 Oct 2020
AbstractforNatural bioactive compounds as a new source of promising G protein-coupled estrogen receptor (GPER) modulators: comprehensive in silico approach | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 347 Views
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Article
In silico approach of naringin as potent phosphatase and tensin homolog (PTEN) protein agonist against prostate cancer
Sankar Muthumanickam, Thangamariyappan Indhumathi, Pandi Boomi, Ramachandran Balajee, Jeyaraman Jeyakanthan, Krishnan Anand, Sundaram Ravikumar, Ponnuchamy Kumar, Arumugam Sudha & Zhihui Jiang
Pages: 1629-1638
Published online: 09 Oct 2020
AbstractforIn silico approach of naringin as potent phosphatase and tensin homolog (PTEN) protein agonist against prostate cancer | Full Text | References | PDF (1.8 MB) | EPUB
  • 421 Views
  • 19 CrossRef citations
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Article
Cysteine focused covalent inhibitors against the main protease of SARS-CoV-2
Archi Sundar Paul, Rajib Islam, Md Rimon Parves, Abdulla Al Mamun, Imrul Shahriar, Md Imran Hossain, Md Nayeem Hossain, Md Ackas Ali & Mohammad A. Halim
Pages: 1639-1658
Published online: 13 Oct 2020
AbstractforCysteine focused covalent inhibitors against the main protease of SARS-CoV-2 | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 3245 Views
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Article
Targeting Imd pathway receptor in Drosophila melanogaster and repurposing of phyto-inhibitors: structural modulation and molecular dynamics
Pankaj Satapathy, Jeevan Kallur Prakash, V. Chirag Gowda, Sunil S. More, Muthuchelian K, Vivek Chandramohan & Farhan Zameer
Pages: 1659-1670
Published online: 14 Oct 2020
AbstractforTargeting Imd pathway receptor in Drosophila melanogaster and repurposing of phyto-inhibitors: structural modulation and molecular dynamics | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 354 Views
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Article
Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study
Maja Vitorović-Todorović, Ilija Cvijetić, Mire Zloh & Andrej Perdih
Pages: 1671-1691
Published online: 13 Oct 2020
AbstractforMolecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 151 Views
  • 1 CrossRef citations
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Article
Molecular dynamics simulations of sulfone derivatives in complex with DNA topoisomerase IIα ATPase domain
Kanika Verma, Panupong Mahalapbutr, Atima Auepattanapong, Onnicha Khaikate, Chutima Kuhakarn, Kaito Takahashi & Thanyada Rungrotmongkol
Pages: 1692-1701
Published online: 22 Oct 2020
AbstractforMolecular dynamics simulations of sulfone derivatives in complex with DNA topoisomerase IIα ATPase domain | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 321 Views
  • 3 CrossRef citations
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Article
Ligand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics
Dhananjay D. Jade, Rajan Pandey, Rakesh Kumar & Dinesh Gupta
Pages: 1702-1718
Published online: 09 Oct 2020
AbstractforLigand-based pharmacophore modeling of TNF-α to design novel inhibitors using virtual screening and molecular dynamics | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 560 Views
  • 5 CrossRef citations
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Article
Antiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection
Vimal K. Maurya, Swatantra Kumar, Madan L. B. Bhatt & Shailendra K. Saxena
Pages: 1719-1735
Published online: 19 Oct 2020
AbstractforAntiviral activity of traditional medicinal plants from Ayurveda against SARS-CoV-2 infection | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 3257 Views
  • 10 CrossRef citations
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Article
Exploring the concerted mechanistic pathway for HIV-1 PR—substrate revealed by umbrella sampling simulation
Zainab K. Sanusi, Monsurat M. Lawal, Pancham Lal. Gupta, Thavendran Govender, Sooraj Baijnath, Tricia Naicker, Glenn E. M. Maguire, Bahareh Honarparvar, Adrian E. Roitberg & Hendrik G. Kruger
Pages: 1736-1747
Published online: 19 Oct 2020
AbstractforExploring the concerted mechanistic pathway for HIV-1 PR—substrate revealed by umbrella sampling simulation | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 422 Views
  • 4 CrossRef citations
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Article
In silico modelling and virtual screening for identification of inhibitors for spore wall protein-5 in Nosema bombycis
Prashantha Karunakar, Saarika P. B.Krishnamurthy V.
Pages: 1748-1763
Published online: 14 Oct 2020
AbstractforIn silico modelling and virtual screening for identification of inhibitors for spore wall protein-5 in Nosema bombycis | Full Text | References | PDF (5 MB) | EPUB
  • 235 Views
  • 1 CrossRef citations
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Article
Molecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19
Anoop Kallingal, Varun Thachan Kundil, Aravind Ayyolath, Abraham Peele Karlapudi, Tomy Muringayil Joseph & Jayadevi Variyar E.
Pages: 1764-1775
Published online: 09 Oct 2020
AbstractforMolecular modeling study of tectoquinone and acteoside from Tectona grandis linn: a new SARS-CoV-2 main protease inhibitor against COVID-19 | Full Text | References | PDF (4.2 MB) | EPUB
  • 2391 Views
  • 8 CrossRef citations
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Article
Investigating the pernicious effects of heparan sulfate in serum amyloid A1 protein aggregation: a structural bioinformatics approach
G. Chandrasekhar & R. Rajasekaran
Pages: 1776-1790
Published online: 14 Oct 2020
AbstractforInvestigating the pernicious effects of heparan sulfate in serum amyloid A1 protein aggregation: a structural bioinformatics approach | Full Text | References | PDF (4.4 MB) | EPUB
  • 138 Views
  • 3 CrossRef citations
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Article
The effect of hesperidin and luteolin isolated from Eriocephalus africanus on apoptosis, cell cycle and miRNA expression in MCF-7
Judie Magura, Roshila Moodley & Irene Mackraj
Pages: 1791-1800
Published online: 14 Oct 2020
AbstractforThe effect of hesperidin and luteolin isolated from Eriocephalus africanus on apoptosis, cell cycle and miRNA expression in MCF-7 | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 365 Views
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Research Article

Article
Therapeutic potential of Chromolaena odorata phyto-constituents against human pancreatic α-amylase
Babatomiwa Kikiowo, Joseph A. Ogunleye, Opeyemi Iwaloye & Taiwo T. Ijatuyi
Pages: 1801-1812
Published online: 15 Oct 2020
AbstractforTherapeutic potential of Chromolaena odorata phyto-constituents against human pancreatic α-amylase | Full Text | References | PDF (2.3 MB) | EPUB
  • 347 Views
  • 16 CrossRef citations
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Research Articles

Article
A computational and bioinformatic analysis of ACE2: an elucidation of its dual role in COVID-19 pathology and finding its associated partners as potential therapeutic targets
Abeedha Tu-Allah Khan, Zumama Khalid, Hafsa Zahid, Muhammad Abrar Yousaf & Abdul Rauf Shakoori
Pages: 1813-1829
Published online: 19 Oct 2020
AbstractforA computational and bioinformatic analysis of ACE2: an elucidation of its dual role in COVID-19 pathology and finding its associated partners as potential therapeutic targets | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 2522 Views
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Article
Structural and functional analysis of Chitinase-IV of Brassica juncea: molecular modeling and dynamic simulation study
Selvaraj Ayyamperumal, Dhananjay Jade, Vyshnavi Tallapaneni, Surender Mohan, Sagar Barge, Nanjan Moola Joghee & Chandrasekar M. J. N.
Pages: 1830-1842
Published online: 28 Oct 2020
AbstractforStructural and functional analysis of Chitinase-IV of Brassica juncea: molecular modeling and dynamic simulation study | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 240 Views
  • 2 CrossRef citations
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Article
Computational analysis of single nucleotide polymorphisms (SNPs) in PPAR gamma associated with obesity, diabetes and cancer
Antony Stalin, Ding Lin, Johnson Josephine Princy, Yue Feng, Haiping Xiang, Savarimuthu Ignacimuthu & Yuan Chen
Pages: 1843-1857
Published online: 22 Oct 2020
AbstractforComputational analysis of single nucleotide polymorphisms (SNPs) in PPAR gamma associated with obesity, diabetes and cancer | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 555 Views
  • 9 CrossRef citations
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Article
Exploring nature’s bounty: identification of Withania somnifera as a promising source of therapeutic agents against COVID-19 by virtual screening and in silico evaluation
Aditi Srivastava, Sahabjada Siddiqui, Rumana Ahmad, Sudhir Mehrotra, Bilal Ahmad & A. N. Srivastava
Pages: 1858-1908
Published online: 27 Nov 2020
AbstractforExploring nature’s bounty: identification of Withania somnifera as a promising source of therapeutic agents against COVID-19 by virtual screening and in silico evaluation | Full Text | References | PDF (16.5 MB) | EPUB | Supplemental
  • 2075 Views
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Review Article

Review Article
From COVID-19 to clot: the involvement of the complement system
Mohamed A. Hendaus & Fatima A. Jomha
Pages: 1909-1914
Published online: 16 Oct 2020
AbstractforFrom COVID-19 to clot: the involvement of the complement system | Full Text | References | PDF (865.9 KB) | EPUB
  • 2505 Views
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Open Access

Correction

Correction
Correction
Pages: i-ii
Published online: 11 Feb 2022
CitationforCorrection | Full Text | PDF (310.3 KB) | EPUB
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