Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 10 (2019)

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Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 10 (2019)

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Research Article

Article
A density functional theory-based analysis of the structural, topological and electronic properties of gemcitabine drug adsorption on the pyrrolidine functionalized single-walled carbon nanotube
Heidar Moradnia, Heidar Raissi & Akbar Bakhtiari
Pages: 2477-2486
Published online: 18 Nov 2018
AbstractforA density functional theory-based analysis of the structural, topological and electronic properties of gemcitabine drug adsorption on the pyrrolidine functionalized single-walled carbon nanotube | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
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Article
Assessment of the chitosan-functionalized graphene oxide as a carrier for loading thioguanine, an antitumor drug and effect of urea on adsorption process: Combination of DFT computational and molecular dynamics simulation studies
Zohre Hasanzade & Heidar Raissi
Pages: 2487-2497
Published online: 01 Nov 2018
AbstractforAssessment of the chitosan-functionalized graphene oxide as a carrier for loading thioguanine, an antitumor drug and effect of urea on adsorption process: Combination of DFT computational and molecular dynamics simulation studies | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 634 Views
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Article
Density functional theory molecular modelling, DNA interactions, antioxidant, antimicrobial, anticancer and biothermodynamic studies of bioactive water soluble mixed ligand complexes
Karunganathan Sakthikumar, Jeyaraj Dhaveethu Raja, Rajadurai Vijay Solomon & Murugesan Sankarganesh
Pages: 2498-2514
Published online: 15 Nov 2018
AbstractforDensity functional theory molecular modelling, DNA interactions, antioxidant, antimicrobial, anticancer and biothermodynamic studies of bioactive water soluble mixed ligand complexes | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 360 Views
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Article
Molecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB)
Sefa Celik, Ali Tugrul Albayrak, Sevim Akyuz & Aysen E. Ozel
Pages: 2515-2526
Published online: 11 Nov 2018
AbstractforMolecular modelling and vibrational investigations of ammonium-based ionic liquid (CLTOAB) | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 506 Views
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Article
Molecular dynamics investigations of structural and functional changes in Bcl-2 induced by the novel antagonist BDA-366
Tao Li, Yinglu Cui & Bian Wu
Pages: 2527-2537
Published online: 10 Dec 2018
AbstractforMolecular dynamics investigations of structural and functional changes in Bcl-2 induced by the novel antagonist BDA-366 | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 417 Views
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Article
Computational insights into the interaction mechanism of transcription cofactor vestigial-like protein 4 binding to TEA domain transcription factor 4 by molecular dynamics simulation and molecular mechanics generalized Born/surface area) calculation
Jian Gao, Yiran Zhang, Han Chen, Qingqing Chen, Dingding Feng, Ling Zhang & Chenglin Li
Pages: 2538-2545
Published online: 09 Nov 2018
AbstractforComputational insights into the interaction mechanism of transcription cofactor vestigial-like protein 4 binding to TEA domain transcription factor 4 by molecular dynamics simulation and molecular mechanics generalized Born/surface area) calculation | Full Text | References | PDF (1.9 MB) | EPUB
  • 254 Views
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Article
Exploring dengue proteome to design an effective epitope-based vaccine against dengue virus
Soudabeh Sabetian, Navid Nezafat, Hesam Dorosti, Mahboubeh Zarei & Younes Ghasemi
Pages: 2546-2563
Published online: 17 Nov 2018
AbstractforExploring dengue proteome to design an effective epitope-based vaccine against dengue virus | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 509 Views
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Article
In silico studying of the whole protein structure and dynamics of Dickkopf family members showed that N-terminal domain of Dickkopf 2 in contrary to other Dickkopfs facilitates its interaction with low density lipoprotein receptor related protein 5/6
Solmaz Sadeghi, Mansour Poorebrahim, Hamzeh Rahimi, Morteza Karimipoor, Kayhan Azadmanesh, Mohammad Reza Khorramizadeh & Ladan Teimoori-Toolabi
Pages: 2564-2580
Published online: 17 Nov 2018
AbstractforIn silico studying of the whole protein structure and dynamics of Dickkopf family members showed that N-terminal domain of Dickkopf 2 in contrary to other Dickkopfs facilitates its interaction with low density lipoprotein receptor related protein 5/6 | Full Text | References | PDF (3.2 MB) | EPUB
  • 271 Views
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Article
Delineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study
M Ramya Chandar Charles, Hsing-Pang Hsieh & Mohane Selvaraj Coumar
Pages: 2581-2592
Published online: 17 Nov 2018
AbstractforDelineating the active site architecture of G9a lysine methyltransferase through substrate and inhibitor binding mode analysis: a molecular dynamics study | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 178 Views
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Article
In silico guided development of imine-based inhibitors for resistance-deriving kinases
Pankaj Kumar Singh & Om Silakari
Pages: 2593-2599
Published online: 20 Nov 2018
AbstractforIn silico guided development of imine-based inhibitors for resistance-deriving kinases | Full Text | References | PDF (1.1 MB) | EPUB | Supplemental
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Letter to the Editor

Letter
Interaction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization
Eduard Tereshkin, Ksenia Tereshkina, Natalia Loiko, Alexei Chulichkov, Vladislav Kovalenko & Yurii Krupyanskii
Pages: 2600-2607
Published online: 04 Nov 2018
AbstractforInteraction of deoxyribonucleic acid with deoxyribonucleic acid-binding protein from starved cells: cluster formation and crystal growing as a model of initial stages of nucleoid biocrystallization | Full Text | References | PDF (2.5 MB) | EPUB
  • 171 Views
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Research Article

Article
Exploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations
Vasavi C.S.Ramasamy Tamizhselvi & Punnagai Munusami
Pages: 2608-2626
Published online: 10 Jan 2019
AbstractforExploring the drug resistance mechanism of active site, non-active site mutations and their cooperative effects in CRF01_AE HIV-1 protease: molecular dynamics simulations and free energy calculations | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 213 Views
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Article
Prediction of matrix metal proteinases-12 inhibitors by machine learning approaches
Bingke Li, Li Hu, Ying Xue, Min Yang, Long Huang, Zhentao Zhang, Jialei Liu & Guowei Deng
Pages: 2627-2640
Published online: 24 Dec 2018
AbstractforPrediction of matrix metal proteinases-12 inhibitors by machine learning approaches | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 239 Views
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Article
In silico site-directed mutagenesis of neutralizing mAb 4C4 and analysis of its interaction with G-H loop of VP1 to explore its therapeutic applications against FMD
Tanmaya Kumar Sahu, Dibyabhaba Pradhan, Atmakuri Ramakrishna Rao & Lingaraj Jena
Pages: 2641-2651
Published online: 15 Nov 2018
AbstractforIn silico site-directed mutagenesis of neutralizing mAb 4C4 and analysis of its interaction with G-H loop of VP1 to explore its therapeutic applications against FMD | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 257 Views
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Article
Proteomics analysis of two heat shock proteins in insects
Samin Seddigh
Pages: 2652-2668
Published online: 17 Nov 2018
AbstractforProteomics analysis of two heat shock proteins in insects | Full Text | References | PDF (5.6 MB) | EPUB
  • 323 Views
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Article
Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L.
Ameya D. Bendre, C. G. Suresh, Dhanasekaran Shanmugam & Sureshkumar Ramasamy
Pages: 2669-2677
Published online: 24 Nov 2018
AbstractforStructural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L. | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 354 Views
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Article
Molecular dynamics and free energy studies on the Drosophila melanogaster and Leptinotarsa decemlineata ecdysone receptor complexed with agonists: Mechanism for binding and selectivity
Fangfang Wang & Bo Zhou
Pages: 2678-2694
Published online: 15 Nov 2018
AbstractforMolecular dynamics and free energy studies on the Drosophila melanogaster and Leptinotarsa decemlineata ecdysone receptor complexed with agonists: Mechanism for binding and selectivity | Full Text | References | PDF (4.2 MB) | EPUB
  • 222 Views
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Article
Structural characterization of a Δ3, Δ2-enoyl-CoA isomerase from Pseudomonas aeruginosa: implications for its involvement in unsaturated fatty acid metabolism
Li Liu, Tao Li, Cui-Ting Peng, Chang-Zhen Sun, Chang-Cheng Li, Qing-Jie Xiao, Li-Hui He, Ning-Yu Wang, Ying-Jie Song, Yi-Bo Zhu, Hong Li, Mei Kang, Hong Tang, Xia Xiong & Rui Bao
Pages: 2695-2702
Published online: 17 Nov 2018
AbstractforStructural characterization of a Δ3, Δ2-enoyl-CoA isomerase from Pseudomonas aeruginosa: implications for its involvement in unsaturated fatty acid metabolism | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 196 Views
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Article
Pharmacophore modeling, multiple docking, and molecular dynamics studies on Wee1 kinase inhibitors
Yanqiu Hu, Lu Zhou, Xiaohong Zhu, Duoqian Dai, Yinfeng Bao & Yaping Qiu
Pages: 2703-2715
Published online: 24 Dec 2018
AbstractforPharmacophore modeling, multiple docking, and molecular dynamics studies on Wee1 kinase inhibitors | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 491 Views
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Opinion Piece

Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research
Ol’ha O. Brovarets’ & Dmytro M. Hovorun
Pages: 2716-2732
Published online: 08 Jan 2019
AbstractforKey microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research | Full Text | References | PDF (2.7 MB) | EPUB
  • 105 Views
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Research Article

Article
Molecular dynamics simulations provide insights into the origin of gleevec’s selectivity toward human tyrosine kinases
Lulu Wang, Guodong Zheng, Xianxian Liu, Duan Ni, Xinheng He, Jinying Cheng & Shaoyong Lu
Pages: 2733-2744
Published online: 01 Nov 2018
AbstractforMolecular dynamics simulations provide insights into the origin of gleevec’s selectivity toward human tyrosine kinases | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 535 Views
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Article
Insights into the effect of molecular crowding on the structure, interactions and functions of siRNA–PAZ complex through molecular dynamics studies
Richa Anand & B. S. Sanjeev
Pages: 2745-2752
Published online: 09 Nov 2018
AbstractforInsights into the effect of molecular crowding on the structure, interactions and functions of siRNA–PAZ complex through molecular dynamics studies | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 173 Views
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