Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 12 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 12 (2023)

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Research Articles

Article
Chlorhexidine as a Keap1-Nrf2 inhibitor: a new target for an old drug for Parkinson's disease therapy
Sruthi Unni, Prashant Deshmukh, Gopinatha Krishnappa, M. M. Srinivas Bharath & Balasundaram Padmanabhan
Pages: 5367-5381
Published online: 17 Jun 2022
AbstractforChlorhexidine as a Keap1-Nrf2 inhibitor: a new target for an old drug for Parkinson's disease therapy | Full Text | References | PDF (3.3 MB) | EPUB
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Article
Synthetic approach toward spiro quinoxaline-β-lactam based heterocyclic compounds: Spectral characterization, SAR, pharmacokinetic and biomolecular interaction studies
Ravi A. Dabhi, Milan P. Dhaduk, Vaibhav D. Bhatt & Bhupesh S. Bhatt
Pages: 5382-5398
Published online: 14 Jun 2022
AbstractforSynthetic approach toward spiro quinoxaline-β-lactam based heterocyclic compounds: Spectral characterization, SAR, pharmacokinetic and biomolecular interaction studies | Full Text | References | PDF (3.1 MB) | EPUB
  • 186 Views
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Article
Inhibition of Mycobacterium tuberculosis InhA (Enoyl-acyl carrier protein reductase) by synthetic Chalcones: a molecular modelling analysis and in-vitro evidence
L. S. Dhivya, Sabarathinam Sarvesh & Ankul Singh S.
Pages: 5399-5417
Published online: 24 Jun 2022
AbstractforInhibition of Mycobacterium tuberculosis InhA (Enoyl-acyl carrier protein reductase) by synthetic Chalcones: a molecular modelling analysis and in-vitro evidence | Full Text | References | PDF (3.6 MB) | EPUB
  • 195 Views
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Article
Identification and prioritization of promising lead molecules from Syzygium aromaticum against Sortase C from Streptococcus pyogenes: an in silico investigation
Purti Mangal, Rajat Kumar Jha, Monika Jain, Amit Kumar Singh & Jayaraman Muthukumaran
Pages: 5418-5435
Published online: 15 Jun 2022
AbstractforIdentification and prioritization of promising lead molecules from Syzygium aromaticum against Sortase C from Streptococcus pyogenes: an in silico investigation | Full Text | References | PDF (4 MB) | EPUB | Supplemental
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Article
Terpenoid analogues as putative therapeutic agents towards glutathione peroxidase (GPX4) in neurodegenerative disorders: a dynamic computational approach
Namrata Sangwan, Jitender Singh, Arushi Chauhan, Ajay Prakash, Krishan L. Khanduja, Bikash Medhi & Pramod K. Avti
Pages: 5436-5446
Published online: 15 Jun 2022
AbstractforTerpenoid analogues as putative therapeutic agents towards glutathione peroxidase (GPX4) in neurodegenerative disorders: a dynamic computational approach | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 212 Views
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Article
Evaluation of the inhibitory potential of Valproic acid against histone deacetylase of Leishmania donovani and computational studies of Valproic acid derivatives
Pragya Prasanna, Tanuja Joshi, Manish Pant, Hemlata Pundir & Subhash Chandra
Pages: 5447-5464
Published online: 15 Jun 2022
AbstractforEvaluation of the inhibitory potential of Valproic acid against histone deacetylase of Leishmania donovani and computational studies of Valproic acid derivatives | Full Text | References | PDF (4.4 MB) | EPUB
  • 255 Views
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Article
A combination strategy of structure-based virtual screening, MM-GBSA, cross docking, molecular dynamics and metadynamics simulations used to investigate natural compounds as potent and specific inhibitors of tumor linked human carbonic anhydrase IX
Varun Chahal & Rita Kakkar
Pages: 5465-5480
Published online: 23 Jun 2022
AbstractforA combination strategy of structure-based virtual screening, MM-GBSA, cross docking, molecular dynamics and metadynamics simulations used to investigate natural compounds as potent and specific inhibitors of tumor linked human carbonic anhydrase IX | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 303 Views
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Article
Intrinsic disorder, extraterrestrial peptides, and prebiotic life on the earth
Prakash Kulkarni, Ravi Salgia & Vladimir N. Uversky
Pages: 5481-5485
Published online: 20 Jun 2022
AbstractforIntrinsic disorder, extraterrestrial peptides, and prebiotic life on the earth | Full Text | References | PDF (832.6 KB) | EPUB
  • 240 Views
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Article
Polyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids
Arshpreet Kaur, Devina Ghai, Vikramaditya G. Yadav, Sandip V. Pawar & Jaspreet K. Sembi
Pages: 5486-5498
Published online: 23 Jun 2022
AbstractforPolyketide synthases (PKSs) of secondary metabolism: in silico identification and characterization in orchids | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 305 Views
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Article
A pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation
Sheikh Abdul Majid, Jan Mohammad Mir, Muzzaffar A. Bhat, Aabid Hussain Shalla, Abhishek Pandey, Taibi Ben Hadda & Magda H. Abdellattif
Pages: 5499-5515
Published online: 24 Jun 2022
AbstractforA pair of carbazate derivatives as novel Schiff base ligands: DFT and POM theory supported spectroscopic and biological evaluation | Full Text | References | PDF (5.2 MB) | EPUB
  • 142 Views
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Article
A combined in vitro–in silico approach for the discovery of novel endogenous enzymatic and ctDNA sequence of bioactive molecules from aerial and root parts of Centaurea sulphurea as antioxidant’s agents
Benhamidat Lyna, Mesli Fouzia, Bensaid Okkacha, Mohammed El Amine Dib & Alain Muselli
Pages: 5516-5537
Published online: 29 Jun 2022
AbstractforA combined in vitro–in silico approach for the discovery of novel endogenous enzymatic and ctDNA sequence of bioactive molecules from aerial and root parts of Centaurea sulphurea as antioxidant’s agents | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 225 Views
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Article
Affinity variation in the interactions of tryptophan- β-cyclodextrin-platinum complex with G-quadruplex and duplex DNAs
Aishwarya Muruganantham, Arokya Nithya Deva Sahayam, Soundarapandian Suganthi, Aleyamma Alexander, Archana Sumohan Pillai & Israel V. M. V. Enoch
Pages: 5538-5547
Published online: 21 Jun 2022
AbstractforAffinity variation in the interactions of tryptophan- β-cyclodextrin-platinum complex with G-quadruplex and duplex DNAs | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 144 Views
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Article
Integrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis
R. Sai Swaroop, P. S. Akhil, Pradhan Sai Sanwid, Prasad Bandana, Rao K. Raksha, Manjunath Meghana, Choudhary Bibha & Venketesh Sivaramakrishnan
Pages: 5548-5567
Published online: 24 Jun 2022
AbstractforIntegrated multi-omic data analysis and validation with yeast model show oxidative phosphorylation modulates protein aggregation in amyotrophic lateral sclerosis | Full Text | References | PDF (5.2 MB) | EPUB | Supplemental
  • 437 Views
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Article
Computational investigation of phytochemicals from Abrus precatorius seeds as modulators of peroxisome proliferator-activated receptor gamma (PPARγ)
Damilola A. Omoboyowa, Gagandeep Singh, John O. Fatoki & Oluwatoba E. Oyeneyin
Pages: 5568-5582
Published online: 30 Jun 2022
AbstractforComputational investigation of phytochemicals from Abrus precatorius seeds as modulators of peroxisome proliferator-activated receptor gamma (PPARγ) | Full Text | References | PDF (3.6 MB) | EPUB
  • 407 Views
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Article
In-silico discovery of inhibitors against human papillomavirus E1 protein
Juliyan Gunasinghe, Siaw San Hwang, Wai Keat Yam, Taufiq Rahman & Xavier Chee Wezen
Pages: 5583-5596
Published online: 24 Jun 2022
AbstractforIn-silico discovery of inhibitors against human papillomavirus E1 protein | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 290 Views
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Article
A new approach used in docking study for predicting the combination drug efficacy in EML4-ALK target of NSCLC
Saleena Younus, S. S. Vinod Chandra, Junaida Ibrahim & Achuth Sankar S. Nair
Pages: 5597-5613
Published online: 13 Jul 2022
AbstractforA new approach used in docking study for predicting the combination drug efficacy in EML4-ALK target of NSCLC | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 304 Views
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Article
A molecular dynamics investigation of N-glycosylation effects on T-cell receptor kinetics
Zachary Rollins, Bradley Harris, Steven George & Roland Faller
Pages: 5614-5623
Published online: 28 Jun 2022
AbstractforA molecular dynamics investigation of N-glycosylation effects on T-cell receptor kinetics | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 314 Views
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Article
Novel insights into the structural changes induced by disease-associated mutations in TDP-43: a computational approach
Abhibhav Sharma & Pinki Dey
Pages: 5624-5634
Published online: 24 Jun 2022
AbstractforNovel insights into the structural changes induced by disease-associated mutations in TDP-43: a computational approach | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 290 Views
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Article
Computational insight into the binding of bryostatin 1 with ferritin: implication of natural compounds in Alzheimer’s disease therapeutics
Moyad Shahwan, Fahad A. Alhumaydhi, Sharaf E. Sharaf, Badrah S. Alghamdi, Saleh Baeesa, Haythum O. Tayeb, Ghulam Md Ashraf & Anas Shamsi
Pages: 5635-5645
Published online: 05 Jul 2022
AbstractforComputational insight into the binding of bryostatin 1 with ferritin: implication of natural compounds in Alzheimer’s disease therapeutics | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 287 Views
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Article
Analysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation
Daniel B. Quintanilha & Hélio F. Dos Santos
Pages: 5646-5659
Published online: 27 Jun 2022
AbstractforAnalysis of Pleurotin binding to human thioredoxin reductase using docking and molecular dynamics simulation | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 341 Views
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Article
PITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer’s disease
Carlton Ranjith Wilson Alphonse, Rajaretinam Rajesh Kannan & Nagasundaram Nagarajan
Pages: 5660-5671
Published online: 24 Jun 2022
AbstractforPITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer’s disease | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 152 Views
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Article
Discovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques
Hisham A. Elrufaie, Linda M. Mohamed, Aya Y. Hamd, Noor A. Bala, Fatima A. Elbadawi, Hiba Ghaboosh & Abdulrahim A. Alzain
Pages: 5672-5684
Published online: 24 Jun 2022
AbstractforDiscovery of novel natural products as rhodesain inhibitors for human African trypanosomiasis using in silico techniques | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 145 Views
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Article
Paracoccidioides brasiliensis plasma membrane characterization by EPR spectroscopy and interactions with amphotericin B, miltefosine and nerolidol
Lais Alonso, Olivia Basso Rocha, Marcos Antônio Batista de Carvalho Junior, Célia Maria de Almeida Soares, Maristela Pereira & Antonio Alonso
Pages: 5685-5695
Published online: 05 Jul 2022
AbstractforParacoccidioides brasiliensis plasma membrane characterization by EPR spectroscopy and interactions with amphotericin B, miltefosine and nerolidol | Full Text | References | PDF (1.6 MB) | EPUB
  • 116 Views
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Article
In silico based multi-epitope vaccine design against norovirus
Pallavi M. Shanthappa, Renuka Suravajhala, Prashanth Suravajhala, Geetha Kumar & Nidheesh Melethadathil
Pages: 5696-5706
Published online: 02 Aug 2022
AbstractforIn silico based multi-epitope vaccine design against norovirus | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 326 Views
  • 2 CrossRef citations
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Article
Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies
Carolina Corrêa Giron, Aatto Laaksonen & Fernando Luís Barroso da Silva
Pages: 5707-5727
Published online: 09 Jul 2022
AbstractforDifferences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 356 Views
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Article
Key interactions of pyrimethamine derivatives specific to wild-type and mutant P. falciparum dihydrofolate reductase based on 3D-QSAR, MD simulations and quantum chemical calculations
Sasipha Seetin, Patchreenart Saparpakorn, Jarunee Vanichtanankul, Danoo Vitsupakorn, Yongyuth Yuthavong, Sumalee Kamchonwongpaisan & Supa Hannongbua
Pages: 5728-5743
Published online: 09 Jul 2022
AbstractforKey interactions of pyrimethamine derivatives specific to wild-type and mutant P. falciparum dihydrofolate reductase based on 3D-QSAR, MD simulations and quantum chemical calculations | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 172 Views
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Article
Prediction of novel and potent inhibitors of lanosterol 14-α demethylase
Mohd Waseem, Jitendra K. Thakur & Naidu Subbarao
Pages: 5744-5756
Published online: 09 Jul 2022
AbstractforPrediction of novel and potent inhibitors of lanosterol 14-α demethylase | Full Text | References | PDF (3.1 MB) | EPUB
  • 274 Views
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Article
In silico homology modeling, docking and sequence analysis of some bacterial laccases to unravel enzymatic specificity towards lignin biodegradation
Monalisa Mahuri, Manish Paul, Sumanta Kumar Sahu & Hrudayanath Thatoi
Pages: 5757-5775
Published online: 15 Jul 2022
AbstractforIn silico homology modeling, docking and sequence analysis of some bacterial laccases to unravel enzymatic specificity towards lignin biodegradation | Full Text | References | PDF (6.4 MB) | EPUB
  • 543 Views
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Article
Biochemical characterization and structure-based in silico screening of potent inhibitor molecules against the 1 cys peroxiredoxin of bacterioferritin comigratory protein family from Candidatus Liberibacter asiaticus
Deena Nath Gupta, Vikram Dalal, Brajesh Kumar Savita, Md Shahid Alam, Anamika Singh, Mrugendra Gubyad, Dilip Kumar Ghosh, Pravindra Kumar & Ashwani Kumar Sharma
Pages: 5776-5788
Published online: 09 Jul 2022
AbstractforBiochemical characterization and structure-based in silico screening of potent inhibitor molecules against the 1 cys peroxiredoxin of bacterioferritin comigratory protein family from Candidatus Liberibacter asiaticus | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 466 Views
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Article
Molecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution
Daniel Ferreira de Lima Neto, Vagner Fonseca, Ronaldo Jesus, Leonardo Hermes Dutra, Layssa Miranda de Oliveria Portela, Carla Freitas, Eduardo Fillizola, Breno Soares, André Luiz de Abreu, Sandeep Twiari, Vasco Azevedo, Aristóteles Goes-Neto, Arnaldo Correia de Medeiros, Norberto Peporine Lopes, Paolo Marinho de Andrade Zanotto & Rodrigo Bentes Kato
Pages: 5789-5801
Published online: 18 Jul 2022
AbstractforMolecular dynamics simulations of the SARS-CoV-2 Spike protein and variants of concern: structural evidence for convergent adaptive evolution | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 386 Views
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Article
Synergistic combination of ritonavir and cisplatin as an efficacious therapy in human cervical cancer cells: a computational drug discovery and in vitro insight
Dayanand Swami, Priyanka Mudaliar, Yash Shrinivas Bichu, Vishal Kumar Sahu, Shine Devarajan, Soumya Basu & Jyotirmoi Aich
Pages: 5802-5816
Published online: 12 Jul 2022
AbstractforSynergistic combination of ritonavir and cisplatin as an efficacious therapy in human cervical cancer cells: a computational drug discovery and in vitro insight | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 323 Views
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Article
Promising disruptors of p53-MDM2 dimerization from some medicinal plant phytochemicals: a molecular modeling study
Abdul-Quddus Kehinde Oyedele, Temitope Isaac Adelusi, Abdeen Tunde Ogunlana, Mojeed Ashiru Ayoola, Rofiat Oluwabusola Adeyemi, Musa Oladayo Babalola, James Babatunde Ayorinde, Josiah Ayoola Isong, Toheeb Olakunle Ajasa & Ibrahim Damilare Boyenle
Pages: 5817-5826
Published online: 13 Jul 2022
AbstractforPromising disruptors of p53-MDM2 dimerization from some medicinal plant phytochemicals: a molecular modeling study | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 324 Views
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Article
Molecular modelling study to discover novel JAK2 signaling pathway inhibitor
Amit Singh & Abha Mishra
Pages: 5827-5838
Published online: 15 Jul 2022
AbstractforMolecular modelling study to discover novel JAK2 signaling pathway inhibitor | Full Text | References | PDF (3.1 MB) | EPUB
  • 239 Views
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Article
Dynamics of lipid displacement inside the hydrophobic cavity of a nonspecific lipid transfer protein from Solanum melongena
Zaid Kamal Madni, Amit Kumar, Ujjwal Kumar, Deepika Jaiswal & Dinakar M. Salunke
Pages: 5839-5849
Published online: 15 Jul 2022
AbstractforDynamics of lipid displacement inside the hydrophobic cavity of a nonspecific lipid transfer protein from Solanum melongena | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 193 Views
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Article
Fructosylation of human insulin causes AGEs formation, structural perturbations and morphological changes: an in silico and multispectroscopic study
Ali Raza, Riaz Mahmood, Safia Habib, Mohd Talha, Shifa Khan, Md Amiruddin Hashmi, Taj Mohammad & Asif Ali
Pages: 5850-5862
Published online: 22 Jul 2022
AbstractforFructosylation of human insulin causes AGEs formation, structural perturbations and morphological changes: an in silico and multispectroscopic study | Full Text | References | PDF (2.7 MB) | EPUB
  • 159 Views
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Article
In vitro and in silico cytotoxic activities of triterpenoids from the leaves of Aralia dasyphylla Miq. and the assessment of their ADMET properties
Hien Nguyen Thi Thu, Duyen Nguyen Huu Huong, Thuan Nguyen Thi Dieu, Hanh Tran Thi Ngoc, Huyen Pham Van, Anh Hoang Thi Ngoc, Ha Nguyen Xuan, Ngoc Khanh Pham, Cuong Nguyen Manh & Phan Nguyen Huu Toan
Pages: 5863-5871
Published online: 15 Jul 2022
AbstractforIn vitro and in silico cytotoxic activities of triterpenoids from the leaves of Aralia dasyphylla Miq. and the assessment of their ADMET properties | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 182 Views
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Article
Investigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations
Kui Xia, Haolei Shen, Peng Wang, Rongri Tan & Damao Xun
Pages: 5872-5881
Published online: 15 Jul 2022
AbstractforInvestigation of the conformation of human prion protein in ethanol solution using molecular dynamics simulations | Full Text | References | PDF (3.6 MB) | EPUB
  • 180 Views
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Article
Interaction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations
Mahdi Rezaei-Sameti & Zohre Iraji Borojeni
Pages: 5882-5893
Published online: 22 Jul 2022
AbstractforInteraction of 5-fluorouracil anticancer drug with nucleobases: insight from DFT, TD-DFT, and AIM calculations | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 238 Views
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Review Article
Therapeutic role of traditionally used Indian medicinal plants and spices in combating COVID-19 pandemic situation
Moumita Nath & Pradip Debnath
Pages: 5894-5913
Published online: 30 Jun 2022
AbstractforTherapeutic role of traditionally used Indian medicinal plants and spices in combating COVID-19 pandemic situation | Full Text | References | PDF (4.7 MB) | EPUB
  • 321 Views
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