Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 2 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 2 (2020)

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Research Articles

Article
Structural insights into the anti-cancer activity of quercetin on G-tetrad, mixed G-tetrad, and G-quadruplex DNA using quantum chemical and molecular dynamics simulations
S. Vinnarasi, R. Radhika, S. Vijayakumar & R. Shankar
Pages: 317-339
Published online: 22 Feb 2019
AbstractforStructural insights into the anti-cancer activity of quercetin on G-tetrad, mixed G-tetrad, and G-quadruplex DNA using quantum chemical and molecular dynamics simulations | Full Text | References | PDF (6.2 MB) | EPUB
  • 639 Views
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Article
Effect of thermostable mutations on the neurotensin receptor 1 (NTSR1) activation state
Shanthi Nagarajan, Nabil J. Alkayed, Sanjiv Kaul & Anthony P. Barnes
Pages: 340-353
Published online: 14 Feb 2019
AbstractforEffect of thermostable mutations on the neurotensin receptor 1 (NTSR1) activation state | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 249 Views
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Article
QSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives
Glaucio Monteiro Ferreira, Juliana Gallottini de Magalhães, Vinícius Gonçalves Maltarollo, Thales Kronenberger, Arasu Ganesan, Flávio da Silva Emery & Gustavo Henrique Goulart Trossini
Pages: 354-363
Published online: 21 Feb 2019
AbstractforQSAR studies on the human sirtuin 2 inhibition by non-covalent 7,5,2-anilinobenzamide derivatives | Full Text | References | PDF (1.6 MB) | EPUB
  • 318 Views
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Article
Determining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study
Louisa Roudini, Negar NayebZadeh Eidgahi, Hamid Reza Rahimi, Mohammad Reza Saberi, Zeinab Amiri Tehranizadeh, Sima Beigoli & Jamshidkhan Chamani
Pages: 364-381
Published online: 17 Feb 2019
AbstractforDetermining the interaction behavior of calf thymus DNA with berberine hydrochloride in the presence of linker histone: a biophysical study | Full Text | References | PDF (2.5 MB) | EPUB
  • 252 Views
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Article
Exploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent
Tara Chand Yadav, Naresh Kumar, Utkarsh Raj, Nidhi Goel, Pritish Kumar Vardawaj, Ramasare Prasad & Vikas Pruthi
Pages: 382-397
Published online: 19 Mar 2019
AbstractforExploration of interaction mechanism of tyrosol as a potent anti-inflammatory agent | Full Text | References | PDF (4.2 MB) | EPUB
  • 409 Views
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Article
Agonism activities of lyso-phosphatidylcholines (LPC) Ligands binding to peroxisome proliferator-activated receptor gamma (PPARγ)
Jiayue Wang, Bohong Wang & Yan Zhang
Pages: 398-409
Published online: 26 Apr 2019
AbstractforAgonism activities of lyso-phosphatidylcholines (LPC) Ligands binding to peroxisome proliferator-activated receptor gamma (PPARγ) | Full Text | References | PDF (2.7 MB) | EPUB
  • 267 Views
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Article
Structural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies
Yongfeng Wan, Shanshan Guan, Mengdan Qian, Houhou Huang, Fei Han, Song Wang & Hao Zhang
Pages: 410-425
Published online: 27 Feb 2019
AbstractforStructural basis of fullerene derivatives as novel potent inhibitors of protein acetylcholinesterase without catalytic active site interaction: insight into the inhibitory mechanism through molecular modeling studies | Full Text | References | PDF (5.4 MB) | EPUB | Supplemental
  • 299 Views
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Article
Delineating the interaction of combretastatin A-4 with αβ tubulin isotypes present in drug resistant human lung carcinoma using a molecular modeling approach
Bajarang Vasant Kumbhar, Vishwambhar Vishnu Bhandare, Dulal Panda & Ambarish Kunwar
Pages: 426-438
Published online: 04 Mar 2019
AbstractforDelineating the interaction of combretastatin A-4 with αβ tubulin isotypes present in drug resistant human lung carcinoma using a molecular modeling approach | Full Text | References | PDF (3.3 MB) | EPUB
  • 398 Views
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Article
Thermodynamic first law efficiency of membrane proteins
Mert Gur, Mert Golcuk, Sema Zeynep Yilmaz & Elhan Taka
Pages: 439-449
Published online: 04 Mar 2019
AbstractforThermodynamic first law efficiency of membrane proteins | Full Text | References | PDF (1.4 MB) | EPUB
  • 650 Views
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Article
Computational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development
Manojit Bhattacharya, Ramesh Chandra Malick, Niladri Mondal, Prasanta Patra, Bibhuti Bhusan Pal, Bidhan Chandra Patra & Basanta Kumar Das
Pages: 450-459
Published online: 07 Apr 2019
AbstractforComputational characterization of epitopic region within the outer membrane protein candidate in Flavobacterium columnare for vaccine development | Full Text | References | PDF (1.4 MB) | EPUB
  • 348 Views
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Article
Effective prediction model and determination of binding residues influential for inhibitors targeting HIV-1 integrase-LEDGF/p75 interface by employing solvent accessible surface area energy as key determinant
Patcharapong Thangsunan, Sakunna Wongsaipun, Sila Kittiwachana & Nuttee Suree
Pages: 460-473
Published online: 27 Feb 2019
AbstractforEffective prediction model and determination of binding residues influential for inhibitors targeting HIV-1 integrase-LEDGF/p75 interface by employing solvent accessible surface area energy as key determinant | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 328 Views
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Article
Experimental and theoretical investigations of novel oxidovanadium(IV) juglone complex: DNA/HSA interaction and cytotoxic activity
Fatemeh Abyar & Leila Tabrizi
Pages: 474-487
Published online: 04 Mar 2019
AbstractforExperimental and theoretical investigations of novel oxidovanadium(IV) juglone complex: DNA/HSA interaction and cytotoxic activity | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 255 Views
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Article
In silico and in vitro studies of transition metal complexes derived from curcumin–isoniazid Schiff base
Porkodi Jeyaraman, Arunadevi Alagarraj & Raman Natarajan
Pages: 488-499
Published online: 02 Apr 2019
AbstractforIn silico and in vitro studies of transition metal complexes derived from curcumin–isoniazid Schiff base | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 393 Views
  • 23 CrossRef citations
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Article
Characterization of medicinal plant-associated biocontrol Bacillus subtilis (SSL2) by liquid chromatography-mass spectrometry and evaluation of compounds by in silico and in vitro methods
Hardik Naik Jinal & Natarajan Amaresan
Pages: 500-510
Published online: 26 Mar 2019
AbstractforCharacterization of medicinal plant-associated biocontrol Bacillus subtilis (SSL2) by liquid chromatography-mass spectrometry and evaluation of compounds by in silico and in vitro methods | Full Text | References | PDF (2.9 MB) | EPUB
  • 262 Views
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Article
Structure based docking and molecular dynamics studies: Peroxisome proliferator-activated receptors –α/γ dual agonists for treatment of metabolic disorders
Virendra Nath, Rohini Agrawal & Vipin Kumar
Pages: 511-523
Published online: 11 Mar 2019
AbstractforStructure based docking and molecular dynamics studies: Peroxisome proliferator-activated receptors –α/γ dual agonists for treatment of metabolic disorders | Full Text | References | PDF (3.7 MB) | EPUB
  • 283 Views
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Article
Membrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations
Yu-Hsien Lien, Dhani Ram Mahato, Felix Hoppe-Seyler & Wolfgang B. Fischer
Pages: 524-532
Published online: 27 Feb 2019
AbstractforMembrane partitioning of peptide aggregates: coarse-grained molecular dynamics simulations | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 374 Views
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Article
Combined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing
Jian Liu, Yehua Zhu, Yufang He, Haohao Zhu, Yi Gao, Zhi Li, Junru Zhu, Xinjie Sun, Fang Fang, Hongmei Wen & Wei Li
Pages: 533-547
Published online: 02 Apr 2019
AbstractforCombined pharmacophore modeling, 3D-QSAR and docking studies to identify novel HDAC inhibitors using drug repurposing | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 563 Views
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Article
Exploring the binding mechanism of saccharin and sodium saccharin to promoter of human p53 gene by theoretical and experimental methods
Mahboubeh Mansourian, Karim Mahnam, Hamid Reza Rajabi, Mahmoud Roushani & Amir Hossein Doustimotlagh
Pages: 548-564
Published online: 11 Mar 2019
AbstractforExploring the binding mechanism of saccharin and sodium saccharin to promoter of human p53 gene by theoretical and experimental methods | Full Text | References | PDF (3.4 MB) | EPUB
  • 314 Views
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Article
Towards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex
Abdulilah Ece
Pages: 565-572
Published online: 11 Mar 2019
AbstractforTowards more effective acetylcholinesterase inhibitors: a comprehensive modelling study based on human acetylcholinesterase protein–drug complex | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 955 Views
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Article
Dual inhibitor design for HIV-1 reverse transcriptase and integrase enzymes: a molecular docking study
Selami Ercan, Berivan Şenyiğit & Yusuf Şenses
Pages: 573-580
Published online: 09 Dec 2019
AbstractforDual inhibitor design for HIV-1 reverse transcriptase and integrase enzymes: a molecular docking study | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 358 Views
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Letters to the Editor

Letter
Integrating molecular dynamics simulation and molecular mechanics/generalized Born surface area calculation into pharmacophore modeling: a case study on the proviral integration site for Moloney murine leukemia virus (Pim)-1 kinase inhibitors
Jian Gao, Yan Wang, Qingqing Chen & Ruosi Yao
Pages: 581-588
Published online: 07 Feb 2019
AbstractforIntegrating molecular dynamics simulation and molecular mechanics/generalized Born surface area calculation into pharmacophore modeling: a case study on the proviral integration site for Moloney murine leukemia virus (Pim)-1 kinase inhibitors | Full Text | References | PDF (2.4 MB) | EPUB
  • 156 Views
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Letter
Molecular mechanism of interactions between chrysin and I-kappa-B kinase epsilon (IKKe)/tank binding kinase-1(TBK1): Cell-based assay and in silico molecular docking studies
M. Amir Siddiqui, Badruddeen, Juber Akhtar, Shahab Uddin M.S.Mohammad Irfan Khan & Mohammad Khalid
Pages: 589-596
Published online: 26 Mar 2019
AbstractforMolecular mechanism of interactions between chrysin and I-kappa-B kinase epsilon (IKKe)/tank binding kinase-1(TBK1): Cell-based assay and in silico molecular docking studies | Full Text | References | PDF (1.8 MB) | EPUB
  • 147 Views
  • 1 CrossRef citations
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Letter
Vorinostat, a possible alternative to metronidazole for the treatment of amebiasis caused by Entamoeba histolytica
S. Montaño, L. A. Constantino-Jonapa, Y. Sixto-López, V. I. Hernández-Ramírez, A. Hernández-Ceruelos, L. C. Romero-Quezada, J. C. Ruvalcaba-Ledezma, P. Talamás-Rohana & L. López-Contreras
Pages: 597-603
Published online: 26 Apr 2019
AbstractforVorinostat, a possible alternative to metronidazole for the treatment of amebiasis caused by Entamoeba histolytica | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 233 Views
  • 1 CrossRef citations
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Letter
Handedness of structural units depends on their mutual arrangement in protein structure
Alexander V. Efimov
Pages: 604-608
Published online: 27 Feb 2019
AbstractforHandedness of structural units depends on their mutual arrangement in protein structure | Full Text | References | PDF (753.2 KB) | EPUB
  • 58 Views
  • 1 CrossRef citations
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Letter
Inhibitory effects of oxali-Platin as a chemotherapeutic drug on the function and structure of bovine liver catalase
Omid Abazari, Adeleh Divsalar & Roohollah Ghobadi
Pages: 609-615
Published online: 11 Mar 2019
AbstractforInhibitory effects of oxali-Platin as a chemotherapeutic drug on the function and structure of bovine liver catalase | Full Text | References | PDF (1.1 MB) | EPUB
  • 181 Views
  • 16 CrossRef citations
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Letter
In vitro and in silico investigation of caprylic acid effect on multi drug resistant (MDR) Klebsiella pneumoniae biofilm
Abhishek Gupta, Lalitha Cheepurupalli, S. Vigneswaran, Sudarshan Singh Rathore, S. Suma Mohan & Jayapradha Ramakrishnan
Pages: 616-624
Published online: 27 Feb 2019
AbstractforIn vitro and in silico investigation of caprylic acid effect on multi drug resistant (MDR) Klebsiella pneumoniae biofilm | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 219 Views
  • 10 CrossRef citations
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Letter
Elucidating the tight-binding mechanism of two oral anticoagulants to factor Xa by using induced-fit docking and molecular dynamics simulation
Qingqing Du, Yan Qian, Xiaojun Yao & Weiwei Xue
Pages: 625-633
Published online: 09 Apr 2019
AbstractforElucidating the tight-binding mechanism of two oral anticoagulants to factor Xa by using induced-fit docking and molecular dynamics simulation | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 422 Views
  • 31 CrossRef citations
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