Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 3 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 3 (2023)

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Research Articles

Article
Analysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET
Mohammed Hadi Ali Al-Jumaili, Farhan Siddique, Faizan Abul Qais, Heba E. Hashem, Samir Chtita, Abida Rani, Muhammad Uzair & Kahtan A. Almzaien
Pages: 765-777
Published online: 03 Dec 2021
AbstractforAnalysis and prediction pathways of natural products and their cytotoxicity against HeLa cell line protein using docking, molecular dynamics and ADMET | Full Text | References | PDF (2.8 MB) | EPUB
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Article
Olive oil-based quercetin nanoemulsion (QuNE)’s interactions with human serum proteins (HSA and HTF) and its anticancer activity
Farnaz Ahmadi Oskooei, Jamshid Mehrzad, Ahmad Asoodeh & Alireza Motavalizadehkakhky
Pages: 778-791
Published online: 17 Dec 2021
AbstractforOlive oil-based quercetin nanoemulsion (QuNE)’s interactions with human serum proteins (HSA and HTF) and its anticancer activity | Full Text | References | PDF (2.9 MB) | EPUB
  • 279 Views
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Article
Engineering non-conserved salt bridges in GH11 xylanase from Bacillus pumilus SSP34 for improved thermal stability: an in-silico evaluation
Sagar Krishna Bhat, Kavya Purushothaman, Appu Rao Gopala Rao Appu Rao & K. Ramachandra Kini
Pages: 792-804
Published online: 08 Dec 2021
AbstractforEngineering non-conserved salt bridges in GH11 xylanase from Bacillus pumilus SSP34 for improved thermal stability: an in-silico evaluation | Full Text | References | PDF (3.9 MB) | EPUB
  • 196 Views
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Article
Synthesis, characterization, and in silico studies of 1,8-naphthyridine derivatives as potential anti-Parkinson’s agents
Madhwi Ojha, Avinash Kumar, Chakrawarti Prasun, Maya S. Nair, Saurabh Chaturvedi, Sarvesh Kumar Paliwal & Sumitra Nain
Pages: 805-820
Published online: 13 Dec 2021
AbstractforSynthesis, characterization, and in silico studies of 1,8-naphthyridine derivatives as potential anti-Parkinson’s agents | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 229 Views
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Article
Computational binding affinity and molecular dynamic characterization of annonaceous acetogenins at nucleotide binding domain (NBD) of multi-drug resistance ATP-binding cassette sub-family B member 1 (ABCB1)
Jeevitha Priya Manoharan, Kavinkumar Nirmala Karunakaran, Subramanian Vidyalakshmi & Karthik Dhananjayan
Pages: 821-832
Published online: 15 Dec 2021
AbstractforComputational binding affinity and molecular dynamic characterization of annonaceous acetogenins at nucleotide binding domain (NBD) of multi-drug resistance ATP-binding cassette sub-family B member 1 (ABCB1) | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 291 Views
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Article
Computational designing of a novel subunit vaccine for human cytomegalovirus by employing the immunoinformatics framework
Abu Tayab Moin, Gagandeep Singh, Nafisa Ahmed, Syeda Afra Saiara, Vladimir I. Timofeev, Nairita Ahsan Faruqui, Shama Sharika Ahsan, Afrida Tabassum, Sadman Sakib Nebir, K. M. Salim Andalib, Yusha Araf, Md. Asad Ullah, Bishajit Sarkar, Nafisa Nawal Islam & Umme Salma Zohora
Pages: 833-855
Published online: 04 Jan 2022
AbstractforComputational designing of a novel subunit vaccine for human cytomegalovirus by employing the immunoinformatics framework | Full Text | References | PDF (5.8 MB) | EPUB | Supplemental
  • 395 Views
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Article
A comprehensive analysis of NAC gene family in Oryza sativa japonica: a structural and functional genomics approach
Sujay Ray, Abishek Basnet, Shreya Bhattacharya, Arundhati Banerjee & Koustav Biswas
Pages: 856-870
Published online: 21 Dec 2021
AbstractforA comprehensive analysis of NAC gene family in Oryza sativa japonica: a structural and functional genomics approach | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 463 Views
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Article
Homology modeling, docking and molecular dynamics studies of some secondary metabolites of actinomycetes as biocontrol agents against the 3HNR enzyme of the phytopathogenic fungus Alternaria alternata
Nedjwa Mansouri, Ouided Benslama & Rabah Arhab
Pages: 871-883
Published online: 11 Dec 2021
AbstractforHomology modeling, docking and molecular dynamics studies of some secondary metabolites of actinomycetes as biocontrol agents against the 3HNR enzyme of the phytopathogenic fungus Alternaria alternata | Full Text | References | PDF (3.5 MB) | EPUB
  • 273 Views
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Article
In silico investigation of the interactions of certain drugs proposed for the treatment of Covid-19 with the paraoxonase-1
Zekeriya Duzgun, Birgül Vanizor Kural, Asim Orem & Ilkay Yildiz
Pages: 884-896
Published online: 13 Dec 2021
AbstractforIn silico investigation of the interactions of certain drugs proposed for the treatment of Covid-19 with the paraoxonase-1 | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 422 Views
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Article
Screening of phytochemicals as potential anti-breast cancer agents targeting HER2: an in-silico approach
Sudarshan Lamichhane, Raj Prateek Rai, Amar Khatri, Rajendra Adhikari, Bhupal Govinda Shrestha & Simon Kumar Shrestha
Pages: 897-911
Published online: 26 Dec 2021
AbstractforScreening of phytochemicals as potential anti-breast cancer agents targeting HER2: an in-silico approach | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 751 Views
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Article
Elucidating the role of N440K mutation in SARS-CoV-2 spike – ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach
Malathi Kullappan, Usha Mary, Jenifer M. Ambrose, Vishnu Priya Veeraraghavan & Krishna Mohan Surapaneni
Pages: 912-929
Published online: 14 Dec 2021
AbstractforElucidating the role of N440K mutation in SARS-CoV-2 spike – ACE-2 binding affinity and COVID-19 severity by virtual screening, molecular docking and dynamics approach | Full Text | References | PDF (3 MB) | EPUB
  • 497 Views
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Article
Computational investigation of potent inhibitors against YsxC: structure-based pharmacophore modeling, molecular docking, molecular dynamics, and binding free energy
Reena Kumari, Ravi Rathi, Seema R. Pathak & Vikram Dalal
Pages: 930-941
Published online: 16 Dec 2021
AbstractforComputational investigation of potent inhibitors against YsxC: structure-based pharmacophore modeling, molecular docking, molecular dynamics, and binding free energy | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 534 Views
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Article
Structural and functional insight into thiazolidinone derivatives as novel candidates for anticancer drug design: in vitro biological and in-silico strategies
Pervaiz Ali Channar, Mubashir Aziz, Syeda Abida Ejaz, Gul-e-Saba Chaudhry, Amna Saeed, Rabail Ujan, Abbas Hasan, Syeda Rabia Ejaz & Aamer Saeed
Pages: 942-953
Published online: 20 Dec 2021
AbstractforStructural and functional insight into thiazolidinone derivatives as novel candidates for anticancer drug design: in vitro biological and in-silico strategies | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 421 Views
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Article
Reverse vaccinology approach to design a vaccine targeting membrane lipoproteins of Salmonella typhi
Saroj Sharma, Vandana Solanki & Vishvanath Tiwari
Pages: 954-969
Published online: 23 Dec 2021
AbstractforReverse vaccinology approach to design a vaccine targeting membrane lipoproteins of Salmonella typhi | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 247 Views
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Article
Investigation on intermolecular interaction of synthesized azo dyes with bovine serum albumin
Hamid Dezhampanah, Asadollah Mohammadi & Amineh Mousazadeh Moghaddam Pour
Pages: 970-981
Published online: 15 Dec 2021
AbstractforInvestigation on intermolecular interaction of synthesized azo dyes with bovine serum albumin | Full Text | References | PDF (2.5 MB) | EPUB
  • 130 Views
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Article
Synthesis, crystallization, XRD, Hirshfeld surface, vibrational spectra, and quantum chemical studies and Computational investigation of Caffeinium bisulfate: a new noncentrosymmetric form
Ramasamy Anitha, Rajaram Sangeetha, Ephrem Arockia Jeya Yasmi Prabha, Jeyachandran Sangavi & Kulanthaivel Langeswaran
Pages: 982-999
Published online: 16 Dec 2021
AbstractforSynthesis, crystallization, XRD, Hirshfeld surface, vibrational spectra, and quantum chemical studies and Computational investigation of Caffeinium bisulfate: a new noncentrosymmetric form | Full Text | References | PDF (3.3 MB) | EPUB
  • 112 Views
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Article
Revealing the drug resistance mechanism of saquinavir due to G48V and V82F mutations in subtype CRF01_AE HIV-1 protease: molecular dynamics simulation and binding free energy calculations
Vasavi C. S.Punnagai Munusami
Pages: 1000-1017
Published online: 17 Dec 2021
AbstractforRevealing the drug resistance mechanism of saquinavir due to G48V and V82F mutations in subtype CRF01_AE HIV-1 protease: molecular dynamics simulation and binding free energy calculations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 128 Views
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Article
Use of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein
G. A. Huerta-Miranda, W. I. García-García, A. Vidal-Limon & M. Miranda-Hernández
Pages: 1018-1027
Published online: 22 Dec 2021
AbstractforUse of simplified models for theoretical prediction of the interactions between available antibodies and the receptor-binding domain of SARS-CoV-2 spike protein | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 173 Views
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Article
CD171 Multi-epitope peptide design based on immuno-informatics approach as a cancer vaccine candidate for glioblastoma
Seyed Amir Hossein Mohammadzadeh Hosseini Moghri, Ghanbar Mahmoodi Chalbatani, Mojtaba Ranjbar, Catarina Raposo & Arefeh Abbasian
Pages: 1028-1040
Published online: 04 Jan 2022
AbstractforCD171 Multi-epitope peptide design based on immuno-informatics approach as a cancer vaccine candidate for glioblastoma | Full Text | References | PDF (2.3 MB) | EPUB
  • 313 Views
  • 1 CrossRef citations
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Article
In silico study of potential immunonutrient-based sports supplements against COVID-19 via targeting ACE2 inhibition using molecular docking and molecular dynamics simulations
Ebrahim Banitalebi, Tooba Abdizadeh, Maryam Khademi Dehkordi, Elham Saghaei & Majid Mardaniyan Ghahfarrokhi
Pages: 1041-1061
Published online: 21 Dec 2021
AbstractforIn silico study of potential immunonutrient-based sports supplements against COVID-19 via targeting ACE2 inhibition using molecular docking and molecular dynamics simulations | Full Text | References | PDF (4.8 MB) | EPUB
  • 248 Views
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Article
An insight into SARS-CoV-2 membrane protein interaction with spike, envelope, and nucleocapsid proteins
Prateek Kumar, Amit Kumar, Neha Garg & Rajanish Giri
Pages: 1062-1071
Published online: 16 Dec 2021
AbstractforAn insight into SARS-CoV-2 membrane protein interaction with spike, envelope, and nucleocapsid proteins | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 881 Views
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Article
Biological, toxicological and molecular docking evaluations of isoxazoline-thiazolidine-2,4-dione analogues as new class of anti-hyperglycemic agents
Saad Fettach, Fatima Zahra Thari, Zakaria Hafidi, Khalid Karrouchi, Kaoutar Bouathmany, Yahia Cherrah, Mohammed El Achouri, Laila Benbacer, Mohammed El Mzibri, Hassan Sefrioui, Khalid Bougrin & My El Abbes Faouzi
Pages: 1072-1084
Published online: 26 Dec 2021
AbstractforBiological, toxicological and molecular docking evaluations of isoxazoline-thiazolidine-2,4-dione analogues as new class of anti-hyperglycemic agents | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 249 Views
  • 6 CrossRef citations
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Article
Binding site hotspot map of PI3Kα and mTOR in the presence of selective and dual ATP-competitive inhibitors
Francisca Fernanda Nunes Azevedo, Francisca Joseli Freitas de Sousa, Francisco Lucas Santos de Oliveira, Jaqueline Vieira Carletti & Geancarlo Zanatta
Pages: 1085-1097
Published online: 16 Dec 2021
AbstractforBinding site hotspot map of PI3Kα and mTOR in the presence of selective and dual ATP-competitive inhibitors | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 199 Views
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Article
Anchoring of Amyloid-β onto Polyunsaturated Phospholipid Membranes
Ruikang Yuan & Haohao Huang
Pages: 1098-1108
Published online: 17 Dec 2021
AbstractforAnchoring of Amyloid-β onto Polyunsaturated Phospholipid Membranes | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 196 Views
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Article
Identification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach
Shristi Modanwal & Nidhi Mishra
Pages: 1109-1127
Published online: 28 Dec 2021
AbstractforIdentification of common genes in obesity and cancer through network interaction and targeting those genes by virtual screening approach | Full Text | References | PDF (6.4 MB) | EPUB
  • 297 Views
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Article
Structural insight on the liquid silk from the middle silk gland of non-mulberry silkworm Antheraea assamensis
Anurupa Goswami & Dipali Devi
Pages: 1128-1139
Published online: 23 Dec 2021
AbstractforStructural insight on the liquid silk from the middle silk gland of non-mulberry silkworm Antheraea assamensis | Full Text | References | PDF (3.1 MB) | EPUB
  • 229 Views
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