Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 8 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 8 (2023)

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Research Articles

Article
An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad
Bibhudutta Mishra, Pranav Ballaney, Gourav Saha, Akshay Shinde, Subhadeep Banerjee, Venkatesan S. Thimmakondu & Raviprasad Aduri
Pages: 3167-3186
Published online: 09 Mar 2022
AbstractforAn in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 343 Views
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Article
In the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II
Satyajit Khatua & Srabani Taraphder
Pages: 3187-3204
Published online: 08 Mar 2022
AbstractforIn the footsteps of an inhibitor unbinding from the active site of human carbonic anhydrase II | Full Text | References | PDF (4.5 MB) | EPUB
  • 496 Views
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Article
Monosaccharide induced temporal delay in cholesterol self-aggregation
Rituparna Hazra & Durba Roy
Pages: 3205-3217
Published online: 07 Mar 2022
AbstractforMonosaccharide induced temporal delay in cholesterol self-aggregation | Full Text | References | PDF (3.9 MB) | EPUB
  • 141 Views
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Article
Thermodynamics of globular protein native structure
Nikolay N. Khechinashvili, Maxim S. Kondratyev & Robert V. Polozov
Pages: 3218-3221
Published online: 29 Mar 2022
AbstractforThermodynamics of globular protein native structure | Full Text | References | PDF (385.3 KB) | EPUB
  • 92 Views
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Article
Vitamin B12 binding to mutated human transcobalamin, in-silico study of TCN2 alanine scanning and ClinVar missense mutations/SNPs
Omar Abuyaman, Ma’mon M. Hatmal, Nawal Hijjawi, Ahmad A. Deeb, Mohammad Abuothman & Mutasem Taha
Pages: 3222-3233
Published online: 09 Mar 2022
AbstractforVitamin B12 binding to mutated human transcobalamin, in-silico study of TCN2 alanine scanning and ClinVar missense mutations/SNPs | Full Text | References | PDF (3 MB) | EPUB
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Article
Exploring electronic, structural and dynamics parameters of phenylbenzothiazole complexes with Mn2+, Cu2+ and Zn2+ for designing new magnetic resonance imaging (MRI) probes: congruence between computation and spectroscopic data
Isael Aparecido Rosa, Mateus A. Gonçalves, Klaus Wilhelm Heinrich Krambrock, Marcelo Henrique dos Santos, Letícia S. Braga, Elaine F. F. da Cunha & Teodorico C. Ramalho
Pages: 3234-3244
Published online: 07 Mar 2022
AbstractforExploring electronic, structural and dynamics parameters of phenylbenzothiazole complexes with Mn2+, Cu2+ and Zn2+ for designing new magnetic resonance imaging (MRI) probes: congruence between computation and spectroscopic data | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 182 Views
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Article
Unbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein
Lokpati Mishra & Tusar Bandyopadhyay
Pages: 3245-3264
Published online: 16 Mar 2022
AbstractforUnbinding of hACE2 and inhibitors from the receptor binding domain of SARS-CoV-2 spike protein | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 213 Views
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Article
In silico and in vitro studies on inhibitors for SARS-CoV-2 non-structural proteins with dual herbal combination of Withania somnifera with five rasayana herbs
Srinivasan Bhargavi, S. R. Madhan Shankar & Christy H. Jemmy
Pages: 3265-3280
Published online: 08 Mar 2022
AbstractforIn silico and in vitro studies on inhibitors for SARS-CoV-2 non-structural proteins with dual herbal combination of Withania somnifera with five rasayana herbs | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 259 Views
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Article
Neem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology
Sutapa Datta, Indrani Sarkar, Gargi Sen & Arnab Sen
Pages: 3281-3294
Published online: 07 Mar 2022
AbstractforNeem and Turmeric in the management of Covid Associated Mucormycosis (CAM) derived through network pharmacology | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 239 Views
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Article
Parallel actin monomers in the 8S complex of actin–INF2
Sanchaita Das, Zixin Zhang, Saichandra Kalvakota, Raul Soto Jr., Martin L. Phillips, Jonathan R. Terman & Emil Reisler
Pages: 3295-3304
Published online: 28 Mar 2022
AbstractforParallel actin monomers in the 8S complex of actin–INF2 | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 306 Views
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Article
Conformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations
Rajarshi Roy, Sayan Poddar, Md Fulbabu Sk & Parimal Kar
Pages: 3305-3320
Published online: 09 Mar 2022
AbstractforConformational preferences of triantennary and tetraantennary hybrid N-glycans in aqueous solution: Insights from 20 μs long atomistic molecular dynamic simulations | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 420 Views
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Article
Computational vaccinology guided design of multi-epitope subunit vaccine against a neglected arbovirus of the Americas
Maria Karolaynne da Silva, Arthur Antunes Coimbra Azevedo, Daniel Melo de Oliveira Campos, Janeusa Trindade de Souto, Umberto Laino Fulco & Jonas Ivan Nobre Oliveira
Pages: 3321-3338
Published online: 14 Mar 2022
AbstractforComputational vaccinology guided design of multi-epitope subunit vaccine against a neglected arbovirus of the Americas | Full Text | References | PDF (3.5 MB) | EPUB
  • 262 Views
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Article
Dealkenylation of neoandrographolide, a phytochemical from Andrographis paniculata stimulates FXR (Farnesoid X Receptor) and enhances gallstone dissolution
Rajani Sharma, Kunal Kumar & Kumari Tanvi
Pages: 3339-3348
Published online: 07 Mar 2022
AbstractforDealkenylation of neoandrographolide, a phytochemical from Andrographis paniculata stimulates FXR (Farnesoid X Receptor) and enhances gallstone dissolution | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 198 Views
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Article
In silico identification of small molecule protein-protein interaction inhibitors: targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein
Jyoti Verma & Naidu Subbarao
Pages: 3349-3367
Published online: 11 Mar 2022
AbstractforIn silico identification of small molecule protein-protein interaction inhibitors: targeting hotspot regions at the interface of MXRA8 and CHIKV envelope protein | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 514 Views
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Article
Computational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein
Tanushree Das & Chaitali Mukhopadhyay
Pages: 3368-3381
Published online: 25 Mar 2022
AbstractforComputational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 228 Views
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Article
Development of peptide vaccine candidate using highly antigenic PE-PGRS family proteins to stimulate the host immune response against Mycobacterium tuberculosis H37Rv: an immuno-informatics approach
Ajit Kumar, Priyanka Sharma, Akanksha Arun & Laxman S. Meena
Pages: 3382-3404
Published online: 16 Mar 2022
AbstractforDevelopment of peptide vaccine candidate using highly antigenic PE-PGRS family proteins to stimulate the host immune response against Mycobacterium tuberculosis H37Rv: an immuno-informatics approach | Full Text | References | PDF (6.8 MB) | EPUB | Supplemental
  • 300 Views
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Article
Identification of tumor homing peptides by utilizing hybrid feature representation
Hongliang Zou, Fan Yang & Zhijian Yin
Pages: 3405-3412
Published online: 09 Mar 2022
AbstractforIdentification of tumor homing peptides by utilizing hybrid feature representation | Full Text | References | PDF (1 MB) | EPUB
  • 136 Views
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Article
Interaction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation
Maliha Nishat, Md. Rakib Hossain, Md. Mehade Hasan, Md. Kamal Hossain, Md. Abul Hossain & Farid Ahmed
Pages: 3413-3429
Published online: 11 Mar 2022
AbstractforInteraction of Anagrelide drug molecule on pristine and doped boron nitride nanocages: a DFT, RDG, PCM and QTAIM investigation | Full Text | References | PDF (5.7 MB) | EPUB | Supplemental
  • 419 Views
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Article
Three-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach
Masoumeh Nosrati & Mahmoud Roushani
Pages: 3430-3439
Published online: 17 Mar 2022
AbstractforThree-dimensional modeling of streptomycin binding single-stranded DNA for aptamer-based biosensors, a molecular dynamics simulation approach | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 519 Views
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Article
Atomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT – a structural computational approach
Divya Sunder Raj, Dinesh Kumar Kesavan, Chidhambara Priya Dharshini Kottaisamy, V. Prasanth Kumar, Waheetha Hopper & Umamaheshwari Sankaran
Pages: 3440-3461
Published online: 16 Mar 2022
AbstractforAtomic level and structural understanding of natural ligands inhibiting Helicobacter pylori peptide deformylase through ligand and receptor based screening, SIFT, molecular dynamics and DFT – a structural computational approach | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 258 Views
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Article
Molecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha
Debojyoti Halder, Subham Das, Alex Joseph & R. S. Jeyaprakash
Pages: 3462-3475
Published online: 14 Mar 2022
AbstractforMolecular docking and dynamics approach to in silico drug repurposing for inflammatory bowels disease by targeting TNF alpha | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 809 Views
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Article
Investigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies
S. Ponkarpagam, K. N. Vennila & Kuppanagounder P. Elango
Pages: 3476-3484
Published online: 14 Mar 2022
AbstractforInvestigating binding of insecticide buprofezin to DNA by experimental and metadynamics simulation studies | Full Text | References | PDF (2.1 MB) | EPUB
  • 203 Views
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Article
Discovery of a novel inhibitor against urokinase-type plasminogen activator, a potential enzyme with a role in atherosclerotic plaque instability
Rik Ganguly, Baphilinia Jones Mylliemngap & Atanu Bhattacharjee
Pages: 3485-3495
Published online: 01 Apr 2022
AbstractforDiscovery of a novel inhibitor against urokinase-type plasminogen activator, a potential enzyme with a role in atherosclerotic plaque instability | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 306 Views
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Article
Exploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow
Merve Yuce, Zehra Sarica, Beril Ates & Ozge Kurkcuoglu
Pages: 3496-3510
Published online: 18 Mar 2022
AbstractforExploring species-specific inhibitors with multiple target sites on S. aureus pyruvate kinase using a computational workflow | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 482 Views
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Article
In-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets
Mousikha Lala, Soumita Bhattacharjee, Chandra Ghosh, Arnab Sen & Indrani Sarkar
Pages: 3511-3523
Published online: 17 Mar 2022
AbstractforIn-silico studies on wild orange (Citrus macroptera Mont.) compounds against COVID-19 pro-inflammation targets | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 181 Views
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Article
Molecular dynamics and 3D-QSAR studies on indazole derivatives as HIF-1α inhibitors
Yogesh Singh, Kulkarni Swanand Sanjay, Pradeep Kumar, Satwinder Singh & Suresh Thareja
Pages: 3524-3541
Published online: 23 Mar 2022
AbstractforMolecular dynamics and 3D-QSAR studies on indazole derivatives as HIF-1α inhibitors | Full Text | References | PDF (12.7 MB) | EPUB
  • 267 Views
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Article
Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2
Aayatti Mallick Gupta, SasthiCharan Mandal, Sukhendu Mandal & Jaydeb Chakrabarti
Pages: 3542-3552
Published online: 16 Mar 2022
AbstractforImmune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2 | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 168 Views
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Article
A closer look at the mode of binding of drug pemetrexed with CT-DNA
S. Ponkarpagam, K. N. Vennila & Kuppanagounder P. Elango
Pages: 3553-3561
Published online: 17 Mar 2022
AbstractforA closer look at the mode of binding of drug pemetrexed with CT-DNA | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 142 Views
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Article
Molecular insights of hyaluronic acid – ethambutol and hyaluronic acid – isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis
R. Thirumalaisamy, V. Aroulmoji, Muhammad Nasir Iqbal, Shreyas Saride, M. Bhuvaneswari, M. Deepa, C. Sivasankar & Riaz Khan
Pages: 3562-3573
Published online: 16 Mar 2022
AbstractforMolecular insights of hyaluronic acid – ethambutol and hyaluronic acid – isoniazid drug conjugates act as promising novel drugs for the treatment of tuberculosis | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 303 Views
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Article
Molecular structure determination, spectroscopic, quantum computational studies and molecular docking of 4-(E)-[2-(benzylamino)phenylimino) methyl-2]ethoxy phenol
Hajam Towseef Ahmad, K. K. Mohammed Ameen, H. Saleem, M. Syed Ali Padusha & F. M. Mashood Ahamed
Pages: 3574-3590
Published online: 23 Mar 2022
AbstractforMolecular structure determination, spectroscopic, quantum computational studies and molecular docking of 4-(E)-[2-(benzylamino)phenylimino) methyl-2]ethoxy phenol | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 332 Views
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Article
Fibroblast growth factor receptor (FGFR) inhibitors as anticancer agents: 3D-QSAR, molecular docking and dynamics simulation studies of 1, 6-naphthyridines and pyridopyrimidines
Dharti H. Modh, Siddharth J. Modi, Hemant Deokar, Savita Yadav & Vithal M. Kulkarni
Pages: 3591-3606
Published online: 23 Mar 2022
AbstractforFibroblast growth factor receptor (FGFR) inhibitors as anticancer agents: 3D-QSAR, molecular docking and dynamics simulation studies of 1, 6-naphthyridines and pyridopyrimidines | Full Text | References | PDF (3.5 MB) | EPUB
  • 229 Views
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Article
Screening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques
Sarah Boumezber & Kemal Yelekçi
Pages: 3607-3629
Published online: 24 Mar 2022
AbstractforScreening of novel and selective inhibitors for neuronal nitric oxide synthase (nNOS) via structure-based drug design techniques | Full Text | References | PDF (5.1 MB) | EPUB
  • 408 Views
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Article
A foundational theoreticalAl12E12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications
Zakir Ullah, Prasad M. Sonawane, Y. Sheena Mary, Y. Shyma Mary, C. Yohannan Panicker & David G. Churchill
Pages: 3630-3646
Published online: 05 Apr 2022
AbstractforA foundational theoreticalAl12E12(E = N, P) adsorption and quinolone docking study: cage–quinolone pairs, optics and possible therapeutic and diagnostic applications | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 278 Views
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Article
Computational investigation of aphid odorant receptor structure and binding function
Cassie Sims, David M. Withall, Neil Oldham, Robert Stockman & Michael Birkett
Pages: 3647-3658
Published online: 30 Mar 2022
AbstractforComputational investigation of aphid odorant receptor structure and binding function | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 711 Views
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Article
Urea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction
Mohd Younus Bhat, Irfan Ahmad Mir, Mahboob Ul Hussain, Laishram Rajendrakumar Singh & Tanveer Ali Dar
Pages: 3659-3666
Published online: 22 Mar 2022
AbstractforUrea ameliorates trimethylamine N-oxide-Induced aggregation of intrinsically disordered α-casein protein: the other side of the urea-methylamine counteraction | Full Text | References | PDF (1.6 MB) | EPUB
  • 243 Views
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Article
Screening of indole derivatives as the potent anticancer agents on dihydrofolate reductase: pharmaco-informatics and molecular dynamics simulation
Behnaz Abdolmaleki & Mina Maddah
Pages: 3667-3679
Published online: 23 Mar 2022
AbstractforScreening of indole derivatives as the potent anticancer agents on dihydrofolate reductase: pharmaco-informatics and molecular dynamics simulation | Full Text | References | PDF (3 MB) | EPUB
  • 164 Views
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Article
De novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico
Andrii A. Zaremba, Polina Y. Zaremba & Maxim O. Platonov
Pages: 3680-3685
Published online: 22 Mar 2022
AbstractforDe novo designed EBAI as a potential inhibitor of the viral protein BHRF1. Research in silico | Full Text | References | PDF (1.4 MB) | EPUB
  • 202 Views
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Article
Elucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches
Roopa Naik & J. Seetharamappa
Pages: 3686-3701
Published online: 24 Mar 2022
AbstractforElucidating the binding mechanism of an antimigraine agent with a model protein: insights from molecular spectroscopic, calorimetric and computational approaches | Full Text | References | PDF (2.9 MB) | EPUB
  • 92 Views
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Article
Exploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD
Showkat Ahmad Mir & Binata Nayak
Pages: 3702-3716
Published online: 28 Mar 2022
AbstractforExploring binding stability of hydroxy-3-(4-hydroxyphenyl)-5-(4-nitrophenyl)-5,5a,7,8,9,9a-hexahydrothiazolo[2,3-b] quinazolin-6-one with T790M/L858R EGFR-TKD | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 143 Views
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