Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 5 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 5 (2021)

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Research Articles

Article
Biophysical insight into the interaction of levocabastine with human serum albumin: spectroscopy and molecular docking approach
Fahad M. Almutairi, Mohammad Rehan Ajmal, Mohammad Khursheed Siddiqi, Nabeela Majid, Adel Ibrahim Ahmad Al-Alawy, Ali Saber Abdelhameed & Rizwan Hasan Khan
Pages: 1525-1534
Published online: 20 Apr 2020
AbstractforBiophysical insight into the interaction of levocabastine with human serum albumin: spectroscopy and molecular docking approach | Full Text | References | PDF (1.7 MB) | EPUB
  • 276 Views
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Article
Protein binding and antioxidant studies of diimine based emissive surfactant–ruthenium(II) complexes
S. Nehru, S. Veeralakshmi, S. Kalaiselvam, S. P. Subin David, J. Sandhya & S. Arunachalam
Pages: 1535-1546
Published online: 02 Mar 2020
AbstractforProtein binding and antioxidant studies of diimine based emissive surfactant–ruthenium(II) complexes | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 238 Views
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Article
Homology modeling, structural insights and in-silico screening for selective inhibitors of mycobacterial CysE
Sunita Gupta & Vibha Gupta
Pages: 1547-1560
Published online: 09 Mar 2020
AbstractforHomology modeling, structural insights and in-silico screening for selective inhibitors of mycobacterial CysE | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 237 Views
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Article
Synthesis of new morpholine containing 3-amido-9-ethylcarbazole derivative and studies on its biophysical interactions with calf thymus DNA/HSA
Fulya Kıpçak, Tugba Taskın Tok, Halil Duyar, Zeynel Seferoğlu & Elmas Gökoğlu
Pages: 1561-1571
Published online: 06 Mar 2020
AbstractforSynthesis of new morpholine containing 3-amido-9-ethylcarbazole derivative and studies on its biophysical interactions with calf thymus DNA/HSA | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 444 Views
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Article
Characterization of VopJ by modelling, docking and molecular dynamics simulation with reference to its role in infection of enteropathogen Vibrio parahaemolyticus
Ishan H. Raval, Rajendra K. Labala, Krishna H. Raval, Shruti Chatterjee & Soumya Haldar
Pages: 1572-1578
Published online: 03 Mar 2020
AbstractforCharacterization of VopJ by modelling, docking and molecular dynamics simulation with reference to its role in infection of enteropathogen Vibrio parahaemolyticus | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 233 Views
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Article
Identification of hot spot residues on serine-arginine protein kinase-1 by molecular dynamics simulation studies
Anshuman Chandra, Nainee Goyal, Imteyaz Qamar & Nagendra Singh
Pages: 1579-1587
Published online: 04 Mar 2020
AbstractforIdentification of hot spot residues on serine-arginine protein kinase-1 by molecular dynamics simulation studies | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 281 Views
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Article
Alanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor
Yalong Cong, Lili Duan, Kaifang Huang, Jinxiao Bao & John Z. H. Zhang
Pages: 1588-1599
Published online: 06 Mar 2020
AbstractforAlanine scanning combined with interaction entropy studying the differences of binding mechanism on HIV-1 and HIV-2 proteases with inhibitor | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 386 Views
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Article
Understanding the mechanism of amygdalin’s multifunctional anti-cancer action using computational approach
Khattab Al-Khafaji & Tugba Taskin Tok
Pages: 1600-1610
Published online: 09 Mar 2020
AbstractforUnderstanding the mechanism of amygdalin’s multifunctional anti-cancer action using computational approach | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 350 Views
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Article
Potential of graphene oxide as a drug delivery system for Sumatriptan: a detailed density functional theory study
Zahra Jafari, Robabeh Baharfar, Ali Shokuhi Rad & Sakineh Asghari
Pages: 1611-1620
Published online: 10 Mar 2020
AbstractforPotential of graphene oxide as a drug delivery system for Sumatriptan: a detailed density functional theory study | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 343 Views
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Article
Conformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases – a computational study
Leonardo Henrique Franca de Lima, Monica Lisa Fernandez-Quintéro, Rafael Eduardo Oliveira Rocha, Diego César Batista Mariano, Raquel Cardoso de Melo-Minardi & Klaus Roman Liedl
Pages: 1621-1634
Published online: 10 Mar 2020
AbstractforConformational flexibility correlates with glucose tolerance for point mutations in β-glucosidases – a computational study | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 382 Views
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Article
Tripolyphosphate crosslinked Triticum aestivum (wheatgrass) functionalized antimicrobial chitosan: Ameliorating effect on physicochemical, mechanical, invitro cytocompatibility and cell migration properties
J. Sandhya, S. Veeralakshmi & S. Kalaiselvam
Pages: 1635-1644
Published online: 12 Mar 2020
AbstractforTripolyphosphate crosslinked Triticum aestivum (wheatgrass) functionalized antimicrobial chitosan: Ameliorating effect on physicochemical, mechanical, invitro cytocompatibility and cell migration properties | Full Text | References | PDF (2.1 MB) | EPUB
  • 157 Views
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Article
Evaluation of a sesquiterpene as possible drug lead against gelatinases via molecular dynamics simulations
Sehrish Jamal, Ayaz Ahmed & Syed Tarique Moin
Pages: 1645-1660
Published online: 25 Mar 2020
AbstractforEvaluation of a sesquiterpene as possible drug lead against gelatinases via molecular dynamics simulations | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 174 Views
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Article
Screening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase
Parth Sarthi Sen Gupta, Rifat Nawaz UI Islam, Sahini Banerjee, Arnab Nayek, Malay Kumar Rana & Amal Kumar Bandyopadhyay
Pages: 1661-1671
Published online: 16 Mar 2020
AbstractforScreening and molecular characterization of lethal mutations of human homogentisate 1, 2 dioxigenase | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 228 Views
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Article
Calcium channel blockers: molecular docking and inhibition studies on carbonic anhydrase I and II isoenzymes
Cüneyt Türkeş, Yeliz Demir & Şükrü Beydemir
Pages: 1672-1680
Published online: 09 Mar 2020
AbstractforCalcium channel blockers: molecular docking and inhibition studies on carbonic anhydrase I and II isoenzymes | Full Text | References | PDF (1.7 MB) | EPUB
  • 801 Views
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Article
Direct effects of low-energy electrons on including sulfur bonds in proteins: a second-order Møller–Plesset perturbation (MP2) theory approach
Nahid Shahabadi, Farshad Shiri, Saba Hadidi & Soheila Kashanian
Pages: 1681-1687
Published online: 19 Mar 2020
AbstractforDirect effects of low-energy electrons on including sulfur bonds in proteins: a second-order Møller–Plesset perturbation (MP2) theory approach | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 74 Views
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Article
Insight of druggable cannabinoids against estrogen receptor β in breast cancer
Arittra Bhattacharjee, Mohammad Uzzal Hossain, Zeshan Mahmud Chowdhury, S. M. Adiat Rahman, Zaied Ahmed Bhuyan, Md. Salimullah & Chaman Ara Keya
Pages: 1688-1697
Published online: 11 Mar 2020
AbstractforInsight of druggable cannabinoids against estrogen receptor β in breast cancer | Full Text | References | PDF (2.5 MB) | EPUB
  • 373 Views
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Article
Structural and functional characterization of chitin binding lectin from Datura stramonium: insights from phylogenetic analysis, protein structure prediction, molecular docking and molecular dynamics simulation
Monika Jain, Jayaraman Muthukumaran & Amit Kumar Singh
Pages: 1698-1716
Published online: 11 Mar 2020
AbstractforStructural and functional characterization of chitin binding lectin from Datura stramonium: insights from phylogenetic analysis, protein structure prediction, molecular docking and molecular dynamics simulation | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 342 Views
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Article
Identification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics
Leily Heidarpoor Saremi, Ali Ebrahimi & Milad Lagzian
Pages: 1717-1734
Published online: 11 Mar 2020
AbstractforIdentification of new potential cyclooxygenase-2 inhibitors: insight from high throughput virtual screening of 18 million compounds combined with molecular dynamic simulation and quantum mechanics | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 293 Views
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Article
Identification of novel insect β-N-acetylhexosaminidase OfHex1 inhibitors based on virtual screening, biological evaluation, and molecular dynamics simulation
Lili Dong, Shengqiang Shen, Yefei Xu, Leng Wang, Qing Yang, Jianjun Zhang & Huizhe Lu
Pages: 1735-1743
Published online: 30 Mar 2020
AbstractforIdentification of novel insect β-N-acetylhexosaminidase OfHex1 inhibitors based on virtual screening, biological evaluation, and molecular dynamics simulation | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 267 Views
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Article
A study on the effects of inhibition mechanism of curcumin, quercetin, and resveratrol on human glutathione reductase through in vitro and in silico approaches
Pınar Güller, Muhammet Karaman, Uğur Güller, Mine Aksoy & Ömer İrfan Küfrevioğlu
Pages: 1744-1753
Published online: 16 Mar 2020
AbstractforA study on the effects of inhibition mechanism of curcumin, quercetin, and resveratrol on human glutathione reductase through in vitro and in silico approaches | Full Text | References | PDF (1.9 MB) | EPUB
  • 744 Views
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Article
Discovery of potential inhibitors for phosphodiesterase 5A, sodium-potassium pump and beta-adrenergic receptor from Terminalia arjuna: in silico approach
Dinanath T. Gaikwad & Namdeo R. Jadhav
Pages: 1754-1765
Published online: 17 Mar 2020
AbstractforDiscovery of potential inhibitors for phosphodiesterase 5A, sodium-potassium pump and beta-adrenergic receptor from Terminalia arjuna: in silico approach | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 159 Views
  • 3 CrossRef citations
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Article
Resveratrol binding to human complement fragment 5a (hC5a) may modulate the C5aR signaling axes
Richa Mishra, Aurosikha Das & Soumendra Rana
Pages: 1766-1780
Published online: 17 Mar 2020
AbstractforResveratrol binding to human complement fragment 5a (hC5a) may modulate the C5aR signaling axes | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 320 Views
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Article
Impact of glioblastoma multiforme associated mutations on the structure and function of MAP/microtubule affinity regulating kinase 4
Ahmad Abu Turab Naqvi, Deeba Shamim Jairajpuri, Afzal Hussain, Gulam Mustafa Hasan, Mohamed F. Alajmi & Md. Imtaiyaz Hassan
Pages: 1781-1794
Published online: 17 Mar 2020
AbstractforImpact of glioblastoma multiforme associated mutations on the structure and function of MAP/microtubule affinity regulating kinase 4 | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 211 Views
  • 7 CrossRef citations
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Article
Molecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease
Thirumal Kumar D, Nikita Jain, Udhaya Kumar S, Prangya Paramita Jena, Siva Ramamoorthy, George Priya Doss C & Hatem Zayed
Pages: 1795-1810
Published online: 31 Mar 2020
AbstractforMolecular dynamics simulations to decipher the structural and functional consequences of pathogenic missense mutations in the galactosylceramidase (GALC) protein causing Krabbe’s disease | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 417 Views
  • 6 CrossRef citations
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Article
Elucidation of molecular interactions between human γD-crystallin and quercetin, an inhibitor against tryptophan oxidation
Shiwani Rana, Sharat Sarmah, Atanu Singha Roy & Kalyan Sundar Ghosh
Pages: 1811-1818
Published online: 18 Mar 2020
AbstractforElucidation of molecular interactions between human γD-crystallin and quercetin, an inhibitor against tryptophan oxidation | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 156 Views
  • 4 CrossRef citations
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Article
In silico identification of novel 5-HT2A antagonists supported with ligand- and target-based drug design methodologies
Milica Radan, Dusan Ruzic, Mirjana Antonijevic, Teodora Djikic & Katarina Nikolic
Pages: 1819-1837
Published online: 17 Mar 2020
AbstractforIn silico identification of novel 5-HT2A antagonists supported with ligand- and target-based drug design methodologies | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 328 Views
  • 8 CrossRef citations
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Article
Evaluation of potential drugs against leishmaniasis targeting catalytic subunit of Leishmania donovani nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches
Deep Bhowmik, Rahul Jagadeesan, Praveen Rai, Rajat Nandi, Kothandan Gugan & Diwakar Kumar
Pages: 1838-1852
Published online: 17 Mar 2020
AbstractforEvaluation of potential drugs against leishmaniasis targeting catalytic subunit of Leishmania donovani nuclear DNA primase using ligand based virtual screening, docking and molecular dynamics approaches | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 478 Views
  • 9 CrossRef citations
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Article
In-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database
Xiao-Yan Feng, Ting-Ting Ding, Ya-Ya Liu, Wei-Ren Xu & Xian-Chao Cheng
Pages: 1853-1864
Published online: 01 Apr 2020
AbstractforIn-silico identification of peroxisome proliferator-activated receptor (PPAR)α/γ agonists from Ligand Expo Components database | Full Text | References | PDF (2.8 MB) | EPUB
  • 240 Views
  • 4 CrossRef citations
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Article
Analyzing organophosphate pesticide-serum albumin binding interaction: a combined STD NMR and molecular docking study
Vandana Dahiya, Bibin G. Anand, Karunakar Kar & Samanwita Pal
Pages: 1865-1878
Published online: 31 Mar 2020
AbstractforAnalyzing organophosphate pesticide-serum albumin binding interaction: a combined STD NMR and molecular docking study | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 380 Views
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Letters to the Editor

Letter
The conformational dynamics of wing gates Ile199 and Phe103 on the binding of dopamine and benzylamine substrates in human monoamine Oxidase B
Subrata Dasgupta, Soumita Mukherjee, Kanakaraj Sekar & Bishnu Prasad Mukhopadhyay
Pages: 1879-1886
Published online: 02 Mar 2020
First Page PreviewforThe conformational dynamics of wing gates Ile199 and Phe103 on the binding of dopamine and benzylamine substrates in human monoamine Oxidase B | Full Text | References | PDF (1.9 MB) | EPUB
  • 130 Views
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Letter
Molecular mechanisms of metal ions in regulating the catalytic efficiency of D-psicose 3-epimerase revealed by multiple short molecular dynamic simulations and free energy predictions
Congcong Li, Jing Wang, Yi Li, Bo Chen, Jin Tao, Xiaoyan Wang, Hengzheng Yang, Yingrui Liu, Yi Tong & Weiwei Han
Pages: 1887-1897
Published online: 23 Mar 2020
AbstractforMolecular mechanisms of metal ions in regulating the catalytic efficiency of D-psicose 3-epimerase revealed by multiple short molecular dynamic simulations and free energy predictions | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 263 Views
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Letter
Mechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi
Faez Iqbal Khan, Fakhrul Hassan, Haider Ali & Dakun Lai
Pages: 1898-1905
Published online: 16 Mar 2020
AbstractforMechanism of pH-induced conformational changes in MurE ligase obtained from Salmonella enterica serovar Typhi | Full Text | References | PDF (3.1 MB) | EPUB
  • 228 Views
  • 6 CrossRef citations
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