Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 15 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 15 (2023)

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Research Articles

Article
Molecular docking study on vitamin D supplements to understand their interaction with VDR-RXRα heterodimer and VDRE of TAGAP gene
M. Shri Preethi, K. Premkumar & S. Asha Devi
Pages: 7009-7018
Published online: 24 Aug 2022
AbstractforMolecular docking study on vitamin D supplements to understand their interaction with VDR-RXRα heterodimer and VDRE of TAGAP gene | Full Text | References | PDF (1.9 MB) | EPUB
  • 250 Views
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Article
Identification of potential inhibitors for N-myristoyltransferase (NMT) protein of Plasmodium vivax
Mariana Sant’Anna Pereira Nicolau, Milllena Almeida Resende, Pedro Serafim, Germano Yoneda Pereira Lima, Carlos Ueira-Vieira, Nilson Nicolau-Junior & Kelly Aparecida Geraldo Yoneyama
Pages: 7019-7031
Published online: 24 Aug 2022
AbstractforIdentification of potential inhibitors for N-myristoyltransferase (NMT) protein of Plasmodium vivax | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 208 Views
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Article
Genomic assortment and interactive insights of the chromosomal encoded control of cell death (ccd) toxin-antitoxin (TA) module in Xenorhabdus nematophila
Shobhi Chaudhary, Mohit Yadav, Shalini Mathpal, Subhash Chandra & Jitendra Singh Rathore
Pages: 7032-7044
Published online: 24 Aug 2022
AbstractforGenomic assortment and interactive insights of the chromosomal encoded control of cell death (ccd) toxin-antitoxin (TA) module in Xenorhabdus nematophila | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 202 Views
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Article
Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases
Hoang Linh Nguyen, Nguyen Quoc Thai & Mai Suan Li
Pages: 7045-7054
Published online: 24 Aug 2022
AbstractforIdentifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 264 Views
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Article
Cupressus sempervirens L. flavonoids as potent inhibitors to xanthine oxidase: in vitro, molecular docking, ADMET and PASS studies
Abderahmane Linani, Talia Serseg, Khedidja Benarous, Leila Bou-salah, Mohamed Yousfi, Mohammed Nabil Alama & Ghulam Md Ashraf
Pages: 7055-7068
Published online: 24 Aug 2022
AbstractforCupressus sempervirens L. flavonoids as potent inhibitors to xanthine oxidase: in vitro, molecular docking, ADMET and PASS studies | Full Text | References | PDF (3.4 MB) | EPUB
  • 299 Views
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Article
In silico and in vitro evaluation of extract derived from Dunaliella salina, a halotolerant microalga for its antifungal and antibacterial activity
Urmilesh Singh, Laxmi  , Prabhakar Singh, Ankit Kumar Singh, Sweksha Singh, Deepak Kumar, Sushant Kumar Shrivastava & Ravi Kumar Asthana
Pages: 7069-7083
Published online: 26 Aug 2022
AbstractforIn silico and in vitro evaluation of extract derived from Dunaliella salina, a halotolerant microalga for its antifungal and antibacterial activity | Full Text | References | PDF (3.6 MB) | EPUB
  • 369 Views
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Article
Design, synthesis, spectroscopic characterization, in-vitro antibacterial evaluation and in-silico analysis of polycaprolactone containing chitosan-quercetin microspheres
Muhammad Azeem, Muhammad Hanif, Khalid Mahmood, Farhan Siddique, Heba E. Hashem, Mubashir Aziz, Nabeela Ameer, Usman Abid, Hafsa Latif, Nasreen Ramzan & Ravi Rawat
Pages: 7084-7103
Published online: 07 Sep 2022
AbstractforDesign, synthesis, spectroscopic characterization, in-vitro antibacterial evaluation and in-silico analysis of polycaprolactone containing chitosan-quercetin microspheres | Full Text | References | PDF (4.7 MB) | EPUB
  • 277 Views
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Article
In silico identification of potential drug-like molecules against G glycoprotein of Nipah virus by molecular docking, DFT studies, and molecular dynamic simulation
Iqra Naeem, Rana Muhammad Mateen, Syed Sibtul Hassan, Asma Tariq, Rukhsana Parveen, Muhammad Arif Nadeem Saqib, Muhammad Irfan Fareed, Mureed Hussain & Muhammad Sohail Afzal
Pages: 7104-7118
Published online: 27 Aug 2022
AbstractforIn silico identification of potential drug-like molecules against G glycoprotein of Nipah virus by molecular docking, DFT studies, and molecular dynamic simulation | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 393 Views
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Article
Significant destabilization of human telomeric G-quadruplex upon peptide binding: dramatic effect of flanking bases
Nikita Kundu, Taniya Sharma, Sarvpreet Kaur, Aman Kumar Mahto, Rikeshwer Prasad Dewangan, J. Shankaraswamy & Sarika Saxena
Pages: 7119-7127
Published online: 29 Aug 2022
AbstractforSignificant destabilization of human telomeric G-quadruplex upon peptide binding: dramatic effect of flanking bases | Full Text | References | PDF (2 MB) | EPUB
  • 147 Views
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Article
Design, synthesis, spectroscopic characterizations, in vitro pancreatic lipase as well as tyrosinase inhibition evaluations and in silico analysis of novel aryl sulfonate-naphthalene hybrids
Adem Korkmaz, Gülbin Kurtay, Esin Kaya & Ercan Bursal
Pages: 7128-7143
Published online: 07 Sep 2022
AbstractforDesign, synthesis, spectroscopic characterizations, in vitro pancreatic lipase as well as tyrosinase inhibition evaluations and in silico analysis of novel aryl sulfonate-naphthalene hybrids | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 652 Views
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Article
Computational investigation of peptidomimetics as potential inhibitors of SARS-CoV-2 spike protein
Mayar Tarek Ibrahim & Peng Tao
Pages: 7144-7157
Published online: 29 Aug 2022
AbstractforComputational investigation of peptidomimetics as potential inhibitors of SARS-CoV-2 spike protein | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 203 Views
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Article
Homology modeling of human BAP1 and analysis of its binding properties through molecular docking and molecular dynamics simulation
Syarifuddin Husain, Ruzianisra Mohamed, Khairul Bariyyah Abd Halim & Siti Syairah Mohd Mutalip
Pages: 7158-7173
Published online: 30 Aug 2022
AbstractforHomology modeling of human BAP1 and analysis of its binding properties through molecular docking and molecular dynamics simulation | Full Text | References | PDF (3.9 MB) | EPUB
  • 234 Views
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Article
Bioinformatics analysis of Muscovy duck parvovirus REP and VP1 proteins
Chi Zhang, Ming Li & Tianfei Yu
Pages: 7174-7189
Published online: 06 Sep 2022
AbstractforBioinformatics analysis of Muscovy duck parvovirus REP and VP1 proteins | Full Text | References | PDF (4.6 MB) | EPUB
  • 198 Views
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Article
Machine learning-based predictive modeling, virtual screening and biological evaluation studies for identification of potential inhibitors of MMP-13
Shahid Parwez, Lalita Panigrahi, Shakil Ahmed & Mohammad Imran Siddiqi
Pages: 7190-7203
Published online: 04 Sep 2022
AbstractforMachine learning-based predictive modeling, virtual screening and biological evaluation studies for identification of potential inhibitors of MMP-13 | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 396 Views
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Article
Biocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study
Asma Talukder, Md. Mijanur Rahman & Md. Habib Ullah Masum
Pages: 7204-7223
Published online: 30 Aug 2022
AbstractforBiocomputational characterisation of MBO_200107 protein of Mycobacterium tuberculosis variant caprae: a molecular docking and simulation study | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 214 Views
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Article
Calculation of binding affinity of JAK1 inhibitors via accurately computational estimation
Thi-Thuy-Huong Le, Linh Hoang Tran, Minh Tam Nguyen, Minh Quan Pham & Huong Thi Thu Phung
Pages: 7224-7234
Published online: 07 Sep 2022
AbstractforCalculation of binding affinity of JAK1 inhibitors via accurately computational estimation | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 124 Views
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Article
Comparative modelling, molecular docking and immobilization studies on Rhizopus oryzae lipase: evaluation of potentials for fatty acid methyl esters synthesis
Zainab Adenike Ayinla, Adedeji Nelson Ademakinwa & Femi Kayode Agboola
Pages: 7235-7247
Published online: 09 Sep 2022
AbstractforComparative modelling, molecular docking and immobilization studies on Rhizopus oryzae lipase: evaluation of potentials for fatty acid methyl esters synthesis | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 260 Views
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Article
Design and in silico analysis of mRNA vaccine construct against Salmonella
Muhammad Janees Imdad, Muhammad Naseem Khan, Hafiz Shahood Alam, Abdul Basit Khan, Zulfiqar Ali Mirani, Adnan Khan & Faraz Ahmed
Pages: 7248-7264
Published online: 12 Sep 2022
AbstractforDesign and in silico analysis of mRNA vaccine construct against Salmonella | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 434 Views
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Article
In silico studies disclose the underlying link between binding affinity and redox potential in laccase isoforms
Kiran Raj Takur, Mayank Kohli, Kajal Pande, Ashish Malik, Apoorva Deshmukh, Abhijit Kayal, Phaneeswara Rao Kommoju & Naveen Kulkarni
Pages: 7265-7276
Published online: 14 Sep 2022
AbstractforIn silico studies disclose the underlying link between binding affinity and redox potential in laccase isoforms | Full Text | References | PDF (3.5 MB) | EPUB
  • 278 Views
  • 1 CrossRef citations
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Article
Promising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA
Ravi Rathi, Reena Kumari, Seema R. Pathak & Vikram Dalal
Pages: 7277-7289
Published online: 08 Sep 2022
AbstractforPromising antibacterials for LLM of Staphylococcus aureus using virtual screening, molecular docking, dynamics, and MMPBSA | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 278 Views
  • 1 CrossRef citations
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Article
Interaction of MnTOEtPyP4 porphyrin with DNA
Gayane V. Ananyan, Yeva B. Dalyan, Nelli H. Karapetyan, Vigen G. Barkhudaryan & Ani A. Avetisyan
Pages: 7290-7296
Published online: 10 Sep 2022
AbstractforInteraction of MnTOEtPyP4 porphyrin with DNA | Full Text | References | PDF (1.1 MB) | EPUB
  • 117 Views
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Article
Antiviral activity of Cenostigma pluviosum var. peltophoroides extract and fractions against SARS-CoV-2
José Renato Pattaro-Júnior, Ingrid Garcia Araújo, Carolina Borsoi Moraes, Cecilia Gomes Barbosa, Gisele Strieder Philippsen, Lúcio Holanda Freitas-Junior, Ana Carolina Guidi, João Carlos Palazzo de Mello, Rosane Marina Peralta, Maria Aparecida Fernandez, Róbson Ricardo Teixeira & Flavio Augusto Vicente Seixas
Pages: 7297-7308
Published online: 07 Sep 2022
AbstractforAntiviral activity of Cenostigma pluviosum var. peltophoroides extract and fractions against SARS-CoV-2 | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 231 Views
  • 4 CrossRef citations
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Article
Elucidating structure and dynamics of glutathione S-transferase from Rhipicephalus (Boophilus) microplus
Warin Rangubpit, Eukote Suwan, Danai Sangthong, Kannika Wongpanit, Roger W. Stich, Prapasiri Pongprayoon & Sathaporn Jittapalapong
Pages: 7309-7317
Published online: 10 Sep 2022
AbstractforElucidating structure and dynamics of glutathione S-transferase from Rhipicephalus (Boophilus) microplus | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 151 Views
  • 1 CrossRef citations
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Article
Binding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study
Vijayakriti Mishra, Arup Kumar Pathak & Tusar Bandyopadhyay
Pages: 7318-7328
Published online: 13 Sep 2022
AbstractforBinding of human serum albumin with uranyl ion at various pH: an all atom molecular dynamics study | Full Text | References | PDF (1.9 MB) | EPUB
  • 138 Views
  • 1 CrossRef citations
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Article
How do the mutations in PfK13 protein promote anti-malarial drug resistance?
Shikha Sharma & Md. Ehesan Ali
Pages: 7329-7338
Published online: 24 Sep 2022
AbstractforHow do the mutations in PfK13 protein promote anti-malarial drug resistance? | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 242 Views
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Article
Fisetin induces apoptosis in human skin cancer cells through downregulating MTH1
Khalid Imtiyaz, Arshad Husain Rahmani, Mohammed A. Alsahli, Saleh A. Almatroodi & M. Moshahid Alam Rizvi
Pages: 7339-7353
Published online: 21 Sep 2022
AbstractforFisetin induces apoptosis in human skin cancer cells through downregulating MTH1 | Full Text | References | PDF (3.9 MB) | EPUB
  • 224 Views
  • 2 CrossRef citations
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Article
Quantum chemical studies on the binding domain of SARS-CoV-2 S-protein: human ACE2 interface complex
Mambatta Haritha & Cherumuttathu H. Suresh
Pages: 7354-7364
Published online: 13 Sep 2022
AbstractforQuantum chemical studies on the binding domain of SARS-CoV-2 S-protein: human ACE2 interface complex | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 212 Views
  • 1 CrossRef citations
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Article
Natural furin inhibitor(s) as potent therapeutic molecule to mitigate SARS-CoV-2 infection
Dhiman Chandra Paul, Minakshi Bhattacharjee, Dhani Ram Mahato & Manash Pratim Sarma
Pages: 7365-7371
Published online: 13 Sep 2022
AbstractforNatural furin inhibitor(s) as potent therapeutic molecule to mitigate SARS-CoV-2 infection | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 125 Views
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Article
Molecular insights into the interaction of apo-lactoferrin with the receptor binding domain of the SARS-CoV-2 spike protein: a molecular dynamics simulation study
Kevion K. Darmawan, Tom C. Karagiannis, Jeff G. Hughes, Darryl M. Small & Andrew Hung
Pages: 7372-7385
Published online: 12 Sep 2022
AbstractforMolecular insights into the interaction of apo-lactoferrin with the receptor binding domain of the SARS-CoV-2 spike protein: a molecular dynamics simulation study | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 203 Views
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Article
Molecular insight of phytocompounds from Indian spices and its hyaluronic acid conjugates to block SARS-CoV-2 viral entry
Karthika Rajamanickam, Thirumalaisamy Rathinavel, Velu Periyannan, Subramanian Ammashi, Shanmugam Marimuthu & Muhammad Nasir Iqbal
Pages: 7386-7405
Published online: 12 Sep 2022
AbstractforMolecular insight of phytocompounds from Indian spices and its hyaluronic acid conjugates to block SARS-CoV-2 viral entry | Full Text | References | PDF (6.8 MB) | EPUB
  • 181 Views
  • 2 CrossRef citations
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Article
Phytochemicals of Cocculus hirsutus deciphered SARS-CoV-2 inhibition by targeting main proteases in molecular docking, simulation, and pharmacological analyses
Mariappan Rajan, Selvakani Prabhakaran, Jyoti Sankar Prusty, Nagendra Chauhan, Prashant Gupta & Awanish Kumar
Pages: 7406-7420
Published online: 13 Sep 2022
AbstractforPhytochemicals of Cocculus hirsutus deciphered SARS-CoV-2 inhibition by targeting main proteases in molecular docking, simulation, and pharmacological analyses | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 212 Views
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Article
Synthesis, antimicrobial properties and in silico studies of aryloxyacetic acid derivatives with hydrazone or thiazolidine-4-one scaffold
Sevil Şenkardeş, Didem Kart, Bilge Bebek, Miyase Gözde Gündüz & Ş Güniz Küçükgüzel
Pages: 7421-7432
Published online: 14 Sep 2022
AbstractforSynthesis, antimicrobial properties and in silico studies of aryloxyacetic acid derivatives with hydrazone or thiazolidine-4-one scaffold | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 486 Views
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Article
Identification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach
Ravi Kant, Prakash Jha, Daman Saluja & Madhu Chopra
Pages: 7433-7446
Published online: 15 Sep 2022
AbstractforIdentification of novel inhibitors of Neisseria gonorrhoeae MurI using homology modeling, structure-based pharmacophore, molecular docking, and molecular dynamics simulation-based approach | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 229 Views
  • 1 CrossRef citations
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Article
Anti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation
M. Oliur Rahman & Sheikh Sunzid Ahmed
Pages: 7447-7462
Published online: 13 Sep 2022
AbstractforAnti-angiogenic potential of bioactive phytochemicals from Helicteres isora targeting VEGFR-2 to fight cancer through molecular docking and molecular dynamics simulation | Full Text | References | PDF (3.8 MB) | EPUB
  • 389 Views
  • 4 CrossRef citations
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Article
Antichagasic evaluation, molecular docking and ADMET properties of the chalcone (2E)-3-(2-fluorophenyl)-1-(2-hydroxy- 3,4,6-trimethoxyphenyl)prop-2-en-1-one against Trypanosoma cruzi
Carlos Henrique Leitão Cavalcante, Francisco Wagner de Queiroz Almeida-Neto, Matheus Nunes da Rocha, Paulo Nogueira Bandeira, Ramon Róseo Paula Pessoa Bezerra de Menezes, Emanuel Paula Magalhães, Tiago Lima Sampaio, Emmanuel Silva Marinho, Márcia Machado Marinho, Alice Maria Costa Martins & Hélcio Silva dos Santos
Pages: 7463-7479
Published online: 19 Sep 2022
AbstractforAntichagasic evaluation, molecular docking and ADMET properties of the chalcone (2E)-3-(2-fluorophenyl)-1-(2-hydroxy- 3,4,6-trimethoxyphenyl)prop-2-en-1-one against Trypanosoma cruzi | Full Text | References | PDF (4 MB) | EPUB
  • 267 Views
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Article
Computational analysis of immunogenic epitopes in the p30 and p54 proteins of African swine fever virus
Mohamed Imdhiyas, Suvam Sen, Nagendra Barman, Lukumoni Buragohain, Yashpal Malik & Sachin Kumar
Pages: 7480-7489
Published online: 23 Sep 2022
AbstractforComputational analysis of immunogenic epitopes in the p30 and p54 proteins of African swine fever virus | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 456 Views
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Review Articles

Review Article
Function identification and characterization of Oryza sativa ZRT and IRT-like proteins computationally for nutrition and biofortification in rice
Khaled Fathy Abdelmotelb Mohammed, Tanushri Kaul, Pawan Kumar Agrawal, Arulprakash Thangaraj, Rashmi Kaul & Sudhir K. Sopory
Pages: 7490-7510
Published online: 16 Sep 2022
AbstractforFunction identification and characterization of Oryza sativa ZRT and IRT-like proteins computationally for nutrition and biofortification in rice | Full Text | References | PDF (6.2 MB) | EPUB | Supplemental
  • 511 Views
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Review Article
Pharmacological features, health benefits and clinical implications of honokiol
Fatima Khatoon, Sabeeha Ali, Vijay Kumar, Abdelbaset Mohamed Elasbali, Hassan H. Alhassan, Salem Hussain Alharethi, Asimul Islam & Md. Imtaiyaz Hassan
Pages: 7511-7533
Published online: 12 Sep 2022
AbstractforPharmacological features, health benefits and clinical implications of honokiol | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 466 Views
  • 6 CrossRef citations
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