Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 6 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 6 (2023)

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Research Articles

Article
Deciphering the role of aquaporin 1 in the adaptation of the stinging catfish Heteropneustes fossilis to environmental hypertonicity by molecular dynamics simulation studies
Priyambada Chutia, Manas Das, Nabajyoti Goswami, Manisha Choudhury, Nirmalendu Saha & Kishore Sarma
Pages: 2075-2089
Published online: 18 Jan 2022
AbstractforDeciphering the role of aquaporin 1 in the adaptation of the stinging catfish Heteropneustes fossilis to environmental hypertonicity by molecular dynamics simulation studies | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 311 Views
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Article
In silico assessment of DNA damage response gene variants associated with head and neck cancer
Raima Das, Sharbadeb Kundu, Shaheen Laskar, Yashmin Choudhury & Sankar Kumar Ghosh
Pages: 2090-2107
Published online: 17 Jan 2022
AbstractforIn silico assessment of DNA damage response gene variants associated with head and neck cancer | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 368 Views
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Article
Insights into the potential of withanolides as Phosphodiesterase-4 (PDE4D) inhibitors
Aditya Rathi, Vipul Kumar & Durai Sundar
Pages: 2108-2117
Published online: 21 Jan 2022
AbstractforInsights into the potential of withanolides as Phosphodiesterase-4 (PDE4D) inhibitors | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 354 Views
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Article
Screening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches
Manisha Pritam, Garima Singh, Rajnish Kumar & Satarudra Prakash Singh
Pages: 2118-2145
Published online: 22 Jan 2022
AbstractforScreening of potential antigens from whole proteome and development of multi-epitope vaccine against Rhizopus delemar using immunoinformatics approaches | Full Text | References | PDF (6.9 MB) | EPUB | Supplemental
  • 442 Views
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Article
Repurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation
Christopher Heng Xuan Ha, Nung Kion Lee, Taufiq Rahman, Siaw San Hwang, Wai Keat Yam & Xavier Wezen Chee
Pages: 2146-2159
Published online: 22 Jan 2022
AbstractforRepurposing FDA-approved drugs as HIV-1 integrase inhibitors: an in silico investigation | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 337 Views
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Article
An in-silico analysis to identify structural, functional and regulatory role of SNPs in hMRE11
Bhoomi Tarapara & Franky Shah
Pages: 2160-2174
Published online: 20 Jan 2022
AbstractforAn in-silico analysis to identify structural, functional and regulatory role of SNPs in hMRE11 | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 335 Views
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Article
Green synthesized silver nanoparticles obtained from Stachys schtschegleevii extract: ct-DNA interaction and in silico and in vitro investigation of antimicrobial activity
Nahid Shahabadi & Mohammad Mahdavi
Pages: 2175-2188
Published online: 20 Jan 2022
AbstractforGreen synthesized silver nanoparticles obtained from Stachys schtschegleevii extract: ct-DNA interaction and in silico and in vitro investigation of antimicrobial activity | Full Text | References | PDF (3.4 MB) | EPUB
  • 270 Views
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Article
In silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli
Samreen , Faizan Abul Qais & Iqbal Ahmad
Pages: 2189-2201
Published online: 22 Jan 2022
AbstractforIn silico screening and in vitro validation of phytocompounds as multidrug efflux pump inhibitor against E. coli | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 647 Views
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Article
Investigation of interaction between dexamethasone/pheniramine and trypsin by fluorescence, UV–vis, CD, and molecular docking
Furkan Calapoglu, Selmihan Sahin, Ismail Ozmen & Sercan Ozbek Yazici
Pages: 2202-2210
Published online: 31 Jan 2022
AbstractforInvestigation of interaction between dexamethasone/pheniramine and trypsin by fluorescence, UV–vis, CD, and molecular docking | Full Text | References | PDF (2.2 MB) | EPUB
  • 291 Views
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Article
Brain DNA damage analysis in pesticide exposed wistar albino rats (Rattus norvegicus): a chemometric approach
Zabin Begum Khoje, Shyam kumarVootla & Muniswamy David
Pages: 2211-2220
Published online: 22 Jan 2022
AbstractforBrain DNA damage analysis in pesticide exposed wistar albino rats (Rattus norvegicus): a chemometric approach | Full Text | References | PDF (1.3 MB) | EPUB
  • 116 Views
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Article
LNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations
Rupak Pal, Indrajit Deb, Joanna Sarzynska & Ansuman Lahiri
Pages: 2221-2230
Published online: 01 Feb 2022
AbstractforLNA-induced dynamic stability in a therapeutic aptamer: insights from molecular dynamics simulations | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 435 Views
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Article
Atomistic mechanism of leptin and leptin-receptor association
Marisol López-Hidalgo, Luis A. Caro-Gómez, Rubí Romo-Rodríguez, Leonardo D. Herrera-Zuñiga, Maricruz Anaya-Reyes, Jorge L. Rosas-Trigueros & Claudia G. Benítez-Cardoza
Pages: 2231-2248
Published online: 25 Jan 2022
AbstractforAtomistic mechanism of leptin and leptin-receptor association | Full Text | References | PDF (5.8 MB) | EPUB
  • 429 Views
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Article
Computational investigations on the potential role of hygrophorones as quorum sensing inhibitors against LasR protein of Pseudomonas aeruginosa
Anu Dalal, Tushar Kushwaha, Gourav Choudhir, Krishna K. Inampudi, Tarak Karmakar, P. Hariprasad & Shivajirao L. Gholap
Pages: 2249-2259
Published online: 25 Jan 2022
AbstractforComputational investigations on the potential role of hygrophorones as quorum sensing inhibitors against LasR protein of Pseudomonas aeruginosa | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 894 Views
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Article
In silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site
Hind Lafridi, Faisal A. Almalki, Taibi Ben Hadda, Malika Berredjem, Sarkar M. A. Kawsar, Ali M. Alqahtani, Eman R. Esharkawy, Brahim Lakhrissi & Hsaine Zgou
Pages: 2260-2273
Published online: 25 Jan 2022
AbstractforIn silico evaluation of molecular interactions between macrocyclic inhibitors with the HCV NS3 protease. Docking and identification of antiviral pharmacophore site | Full Text | References | PDF (3.3 MB) | EPUB
  • 187 Views
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Article
Hypoglycemic and hepatoprotective effects in adult zebrafish (Danio rerio) of fisetinidol isolated from Bauhinia pentandra: In vivo and in silico assays
Horlando Carlota da Silva, Aurelio de Oliveira Monteiro, Francisco Wagner de Queiroz Almeida-Neto, Emanuelle Machado Marinho, Maria Kueirislene Amâncio Ferreira, Francisco Rogênio da Silva Mendes, Emmanuel Silva Marinho, Márcia Machado Marinho, Lucas Lima Bezerra, Matheus Nunes da Rocha, Jane Eire Silva Alencar de Menezes, Alexandre Magno Rodrigues Teixeira, Antonio Wlisses da Silva, Emanuela de Lima Rebouças, Francisco das Chagas Lima Pinto, Hélcio Silva dos Santos & Gilvandete Maria Pinheiro Santiago
Pages: 2274-2288
Published online: 22 Jan 2022
AbstractforHypoglycemic and hepatoprotective effects in adult zebrafish (Danio rerio) of fisetinidol isolated from Bauhinia pentandra: In vivo and in silico assays | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 435 Views
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Article
Designing of nanobodies against Dengue virus Capsid: a computational affinity maturation approach
Dwaipayan Chaudhuri, Satyabrata Majumder, Joyeeta Datta & Kalyan Giri
Pages: 2289-2299
Published online: 22 Jan 2022
AbstractforDesigning of nanobodies against Dengue virus Capsid: a computational affinity maturation approach | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 483 Views
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Article
In vitro cytotoxicity, antibacterial activity and HSA and ct-DNA interaction studies of chlorogenic acid loaded on γ-Fe2O3@SiO2 as new nanoparticles
Nahid Shahabadi, Alireza Akbari, Fatemeh Karampour, Monireh Falsafi & Saba Zendehcheshm
Pages: 2300-2320
Published online: 04 Feb 2022
AbstractforIn vitro cytotoxicity, antibacterial activity and HSA and ct-DNA interaction studies of chlorogenic acid loaded on γ-Fe2O3@SiO2 as new nanoparticles | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 172 Views
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Article
In vitro oxidation of hispidin and gallic acid by horseradish peroxidase
Damian Tarasek, Hubert Wojtasek, Khedidja Benarous & Mohamed Yousfi
Pages: 2321-2325
Published online: 22 Jan 2022
AbstractforIn vitro oxidation of hispidin and gallic acid by horseradish peroxidase | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 194 Views
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Article
Structural exploration of selected C6 and C7-substituted coumarin isomers as selective MAO-B inhibitors
Yassir Boulaamane, Iqrar Ahmad, Harun Patel, Niloy Das, Mohammed Reda Britel & Amal Maurady
Pages: 2326-2340
Published online: 15 Feb 2022
AbstractforStructural exploration of selected C6 and C7-substituted coumarin isomers as selective MAO-B inhibitors | Full Text | References | PDF (4.5 MB) | EPUB
  • 332 Views
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Article
Exploring the role of framework mutations in enabling breadth of a cross-reactive antibody (CR3022) against the SARS-CoV-2 RBD and its variants of concern
Samvedna Saini, Manusmriti Agarwal, Amartya Pradhan, Savitha Pareek, Ashish K Singh, Gagan Dhawan, Uma Dhawan & Yatender Kumar
Pages: 2341-2354
Published online: 31 Jan 2022
AbstractforExploring the role of framework mutations in enabling breadth of a cross-reactive antibody (CR3022) against the SARS-CoV-2 RBD and its variants of concern | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 424 Views
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Article
Artecanin of Laurus nobilis is a novel inhibitor of SARS-CoV-2 main protease with highly desirable druglikeness
Mohammed Baqur S. Al-Shuhaib, Hayder O. Hashim, Jafar M. B. Al-Shuhaib & Daniel H. Obayes
Pages: 2355-2367
Published online: 22 Jan 2022
AbstractforArtecanin of Laurus nobilis is a novel inhibitor of SARS-CoV-2 main protease with highly desirable druglikeness | Full Text | References | PDF (2 MB) | EPUB
  • 184 Views
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Article
Mutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor
Gatta K. R. S. Naresh & Lalitha Guruprasad
Pages: 2368-2381
Published online: 03 Feb 2022
AbstractforMutations in the receptor-binding domain of human SARS CoV-2 spike protein increases its affinity to bind human ACE-2 receptor | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 261 Views
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Article
Excavating phytochemicals from plants possessing antiviral activities for identifying SARS-CoV hemagglutinin-esterase inhibitors by diligent computational workflow
Chirag N. Patel, Dweipayan Goswami, Dharmesh G. Jaiswal, Siddhi P. Jani, Robin M. Parmar, Rakesh M. Rawal & Himanshu A. Pandya
Pages: 2382-2397
Published online: 31 Jan 2022
AbstractforExcavating phytochemicals from plants possessing antiviral activities for identifying SARS-CoV hemagglutinin-esterase inhibitors by diligent computational workflow | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 262 Views
  • 3 CrossRef citations
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Article
Computational approaches for evaluation of isobavachin as potential inhibitor against t877a and w741l mutations in prostate cancer
Rene Barbie Browne, Nabajyoti Goswami, Probodh Borah & Jayanti Datta Roy
Pages: 2398-2418
Published online: 04 Feb 2022
AbstractforComputational approaches for evaluation of isobavachin as potential inhibitor against t877a and w741l mutations in prostate cancer | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 243 Views
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Article
Deciphering the molecular mechanisms of selective non-covalency demonstrated differentially by 9-Allylnaphtho[1,8-ef]isoindole-7,8,10(9H)-trione (C11) against fibroblast growth factor receptors 1–4
Fisayo A. Olotu & Mahmoud E. S. Soliman
Pages: 2419-2430
Published online: 02 Feb 2022
AbstractforDeciphering the molecular mechanisms of selective non-covalency demonstrated differentially by 9-Allylnaphtho[1,8-ef]isoindole-7,8,10(9H)-trione (C11) against fibroblast growth factor receptors 1–4 | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 185 Views
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Article
Inhibition and disintegration of Bacillus subtilis biofilm with small molecule inhibitors identified through virtual screening for targeting TasA(28-261), the major protein component of ECM
Nidhi Verma, Shubham Srivastava, Ruchi Malik, Pankaj Goyal & Janmejay Pandey
Pages: 2431-2447
Published online: 31 Jan 2022
AbstractforInhibition and disintegration of Bacillus subtilis biofilm with small molecule inhibitors identified through virtual screening for targeting TasA(28-261), the major protein component of ECM | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 265 Views
  • 2 CrossRef citations
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Article
In-silico investigation of some recent natural compounds for their potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study
Taner Erdogan
Pages: 2448-2465
Published online: 28 Jan 2022
AbstractforIn-silico investigation of some recent natural compounds for their potential use against SARS-CoV-2: a DFT, molecular docking and molecular dynamics study | Full Text | References | PDF (7.1 MB) | EPUB | Supplemental
  • 304 Views
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Article
Molecular dynamics simulations of aqueous systems of inhibitor candidates for adenosine-5’-phosphosufate reductase
Talis Uelisson da Silva, Karina de Carvalho Pougy, Magaly Girão Albuquerque, Camilo Henrique da Silva Lima & Sérgio de Paula Machado
Pages: 2466-2477
Published online: 01 Feb 2022
AbstractforMolecular dynamics simulations of aqueous systems of inhibitor candidates for adenosine-5’-phosphosufate reductase | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 252 Views
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Article
The molecular docking and molecular dynamics study of flavonol synthase and flavonoid 3’-monooxygenase enzymes involved for the enrichment of kaempferol
Garima Kumari, Vinod Kumar Nigam & Dev Mani Pandey
Pages: 2478-2491
Published online: 02 Feb 2022
AbstractforThe molecular docking and molecular dynamics study of flavonol synthase and flavonoid 3’-monooxygenase enzymes involved for the enrichment of kaempferol | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 474 Views
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Article
Synthesis, molecular docking, molecular dynamics and evaluation of Drug-Likeness properties of the fused N-Formyl pyrazoline substituted new dehydroepiandrosterone derivatives
İrfan Çapan, Abdulmalik Shehu, Yusuf Sert, İsmail Çelik, Meryem Erol, İrfan Koca & Süleyman Servi
Pages: 2492-2503
Published online: 08 Feb 2022
AbstractforSynthesis, molecular docking, molecular dynamics and evaluation of Drug-Likeness properties of the fused N-Formyl pyrazoline substituted new dehydroepiandrosterone derivatives | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 525 Views
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Article
Distribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn (Hippophae salicifolia)
Parneeta Chaudhary & Prakash Chand Sharma
Pages: 2504-2517
Published online: 04 Feb 2022
AbstractforDistribution of simple sequence repeats, transcription factors, and differentially expressed genes in the NGS-based transcriptome of male and female seabuckthorn (Hippophae salicifolia) | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 203 Views
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Article
Accelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBD
Abd Al-Aziz A. Abu-Saleh, Arpita Yadav & Raymond A. Poirier
Pages: 2518-2527
Published online: 08 Feb 2022
AbstractforAccelerating the discovery of the beyond rule of five compounds that have high affinities toward SARS-CoV-2 spike RBD | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 171 Views
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Article
Enabling CT-Scans for covid detection using transfer learning-based neural networks
Ankit Kumar Dubey & Krishna Kumar Mohbey
Pages: 2528-2539
Published online: 06 Feb 2022
AbstractforEnabling CT-Scans for covid detection using transfer learning-based neural networks | Full Text | References | PDF (2.6 MB) | EPUB
  • 276 Views
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Article
Computational studies on the cholinesterase, beta-secretase 1 (BACE1) and monoamine oxidase (MAO) inhibitory activities of endophytes-derived compounds: towards discovery of novel neurotherapeutics
Ayodeji Osmund Falade, Kayode Ezekiel Adewole, Ahmed Adebayo Ishola, Gideon Ampoma Gyebi & Nurudeen Rasaq Olajide
Pages: 2540-2554
Published online: 04 Feb 2022
AbstractforComputational studies on the cholinesterase, beta-secretase 1 (BACE1) and monoamine oxidase (MAO) inhibitory activities of endophytes-derived compounds: towards discovery of novel neurotherapeutics | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 266 Views
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Article
Computational investigation of the alkaloids of Pilocarpus microphyllus species as phytopharmaceuticals for the inhibition of sterol 14α-demethylase protease of Trypanosoma cruzi
Ézio R. A. de Sá, Janilson L. Souza, Rayla K. M. Costa, Rômulo O. Barros, Carlos E. B. de Lima, Francisco das C. A. Lima & Ricardo M. Ramos
Pages: 2555-2573
Published online: 08 Feb 2022
AbstractforComputational investigation of the alkaloids of Pilocarpus microphyllus species as phytopharmaceuticals for the inhibition of sterol 14α-demethylase protease of Trypanosoma cruzi | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 349 Views
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Article
Elucidating the inhibitory mechanism of yeast α-glucosidase by phytocompounds from Scoparia dulcis through in vitro and in silico approach
Gopinath Murugan, Divya Sangeetha Rajkumar, Malarvizhi Kaliyaperumal, Ramya Ramdoss, Sasirekha Natarajan & Rajashree Padmanaban
Pages: 2574-2586
Published online: 02 Feb 2022
AbstractforElucidating the inhibitory mechanism of yeast α-glucosidase by phytocompounds from Scoparia dulcis through in vitro and in silico approach | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 249 Views
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Article
Bioinformatic characterization of a triacylglycerol lipase produced by Aspergillus flavus isolated from the decaying seed of Cucumeropsis mannii
Benjamin. O. Ezema, Kingsley. O. Omeje, Roslyn M. Bill, Alan D. Goddard, Sabinus Oscar O. Eze & Alfred Fernandez-Castane
Pages: 2587-2601
Published online: 11 Feb 2022
AbstractforBioinformatic characterization of a triacylglycerol lipase produced by Aspergillus flavus isolated from the decaying seed of Cucumeropsis mannii | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 3099 Views
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Open Access

Review Article

Review Article
Discovery of compounds inhibiting SARS-COV-2 multi-targets
Santanu Sasidharan, Neellohit Sarkar & Prakash Saudagar
Pages: 2602-2617
Published online: 07 Jan 2022
AbstractforDiscovery of compounds inhibiting SARS-COV-2 multi-targets | Full Text | References | PDF (1.9 MB) | EPUB
  • 322 Views
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