Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 8 (2016)

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Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 8 (2016)

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Research Articles

Article
Hydrogen bonds in Zif268 proteins – a theoretical perspective
Umadevi Palanivel & Senthilkumar Lakshmipathi
Pages: 1607-1624
Published online: 20 Oct 2015
AbstractforHydrogen bonds in Zif268 proteins – a theoretical perspective | Full Text | References | PDF (2.6 MB) | Supplemental
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Article
Reactive oxygen species and energy machinery: an integrated dynamic model
Kalyani Korla
Pages: 1625-1640
Published online: 29 Sep 2015
AbstractforReactive oxygen species and energy machinery: an integrated dynamic model | Full Text | References | PDF (1.2 MB)
  • 148 Views
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Article
Acytota – associated kingdom of neglected life
Edward N. Trifonov & Eduard Kejnovsky
Pages: 1641-1648
Published online: 01 Mar 2016
AbstractforAcytota – associated kingdom of neglected life | Full Text | References | PDF (219.4 KB)
  • 230 Views
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Article
Analysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes
Sunil Kanti Mondal, Sudip Kundu, Rabindranath Das & Sujit Roy
Pages: 1649-1666
Published online: 28 Sep 2015
AbstractforAnalysis of phylogeny and codon usage bias and relationship of GC content, amino acid composition with expression of the structural nif genes | Full Text | References | PDF (1.3 MB)
  • 293 Views
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Article
Progesterone 5β-reductases/iridoid synthases (PRISE): gatekeeper role of highly conserved phenylalanines in substrate preference and trapping is supported by molecular dynamics simulations
Jan Petersen, Harald Lanig, Jennifer Munkert, Peter Bauer, Frieder Müller-Uri & Wolfgang Kreis
Pages: 1667-1680
Published online: 12 Oct 2015
AbstractforProgesterone 5β-reductases/iridoid synthases (PRISE): gatekeeper role of highly conserved phenylalanines in substrate preference and trapping is supported by molecular dynamics simulations | Full Text | References | PDF (724.5 KB) | Supplemental
  • 241 Views
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Article
Cloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus
Vashni Gramany, Faez Iqbal Khan, Algasan Govender, Krishna Bisetty, Suren Singh & Kugenthiren Permaul
Pages: 1681-1692
Published online: 19 Oct 2015
AbstractforCloning, expression, and molecular dynamics simulations of a xylosidase obtained from Thermomyces lanuginosus | Full Text | References | PDF (691.1 KB)
  • 458 Views
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Article
Interaction of a tyrosine kinase inhibitor, vandetanib with human serum albumin as studied by fluorescence quenching and molecular docking
Md. Zahirul Kabir, Shevin R. Feroz, Abdul Kadir Mukarram, Zazali Alias, Saharuddin B. Mohamad & Saad Tayyab
Pages: 1693-1704
Published online: 27 Jan 2016
AbstractforInteraction of a tyrosine kinase inhibitor, vandetanib with human serum albumin as studied by fluorescence quenching and molecular docking | Full Text | References | PDF (553.6 KB) | Supplemental
  • 324 Views
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Article
Model-aided atpE gene knockout strategy in Escherichia coli for enhanced succinic acid production from glycerol
Bashir Sajo Mienda, Mohd Shahir Shamsir & Rosli Md. Illias
Pages: 1705-1716
Published online: 10 Dec 2015
AbstractforModel-aided atpE gene knockout strategy in Escherichia coli for enhanced succinic acid production from glycerol | Full Text | References | PDF (503.2 KB) | Supplemental
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Article
Estimating binding free energy of a putative growth factors EGF–VEGF complex – a computational bioanalytical study
Meng-Han Lin, C. Allen Chang & Wolfgang B. Fischer
Pages: 1717-1724
Published online: 18 Nov 2015
AbstractforEstimating binding free energy of a putative growth factors EGF–VEGF complex – a computational bioanalytical study | Full Text | References | PDF (567.3 KB) | Supplemental
  • 126 Views
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Article
KCTD5 is endowed with large, functionally relevant, interdomain motions
Daniela Barone, Nicole Balasco & Luigi Vitagliano
Pages: 1725-1735
Published online: 19 Oct 2015
AbstractforKCTD5 is endowed with large, functionally relevant, interdomain motions | Full Text | References | PDF (1,005.4 KB) | Supplemental
  • 196 Views
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Article
Computational screening and characterization of putative vaccine candidates of Plasmodium vivax
Y. Nanda Kumar, G. Jeyakodi, K. Gunasekaran & P. Jambulingam
Pages: 1736-1750
Published online: 29 Oct 2015
AbstractforComputational screening and characterization of putative vaccine candidates of Plasmodium vivax | Full Text | References | PDF (817.3 KB) | Supplemental
  • 252 Views
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Article
Synthesis, cytotoxicity assessment, and interaction and docking of novel palladium(II) complexes of imidazole derivatives with human serum albumin
Mahboube Eslami Moghadam, Adeleh Divsalar, Abdolghafar Abolhosseini Shahrnoy & Ali Akbar Saboury
Pages: 1751-1762
Published online: 20 Oct 2015
AbstractforSynthesis, cytotoxicity assessment, and interaction and docking of novel palladium(II) complexes of imidazole derivatives with human serum albumin | Full Text | References | PDF (962.9 KB)
  • 340 Views
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Article
Effects of cadmium on the cuttlefish Sepia pharaonis’ arginine kinase: unfolding kinetics integrated with computational simulations
Yue-Xiu Si, Jinhyuk Lee, Feng Zhao, Shang-Jun Yin, Yong-Doo Park, Guo-Ying Qian & Xia-Min Jiang
Pages: 1763-1777
Published online: 19 Oct 2015
AbstractforEffects of cadmium on the cuttlefish Sepia pharaonis’ arginine kinase: unfolding kinetics integrated with computational simulations | Full Text | References | PDF (1.1 MB)
  • 191 Views
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Article
Allosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination
Nidhi Rani, Saravanan Vijayakumar, Lakshmi P.T.V.Annamalai Arunachalam
Pages: 1778-1796
Published online: 04 May 2016
AbstractforAllosteric site-mediated active site inhibition of PBP2a using Quercetin 3-O-rutinoside and its combination | Full Text | References | PDF (1.6 MB)
  • 338 Views
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Article
Molecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT
Akram Izadyar, Nafiseh Farhadian & Naser Chenarani
Pages: 1797-1805
Published online: 24 Nov 2015
AbstractforMolecular dynamics simulation of doxorubicin adsorption on a bundle of functionalized CNT | Full Text | References | PDF (803.1 KB)
  • 409 Views
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Article
Structural modeling of HLA-B*1502/peptide/carbamazepine/T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis
Peng Zhou, Shilei Zhang, Yewang Wang, Chao Yang & Jian Huang
Pages: 1806-1817
Published online: 14 Dec 2015
AbstractforStructural modeling of HLA-B*1502/peptide/carbamazepine/T-cell receptor complex architecture: implication for the molecular mechanism of carbamazepine-induced Stevens-Johnson syndrome/toxic epidermal necrolysis | Full Text | References | PDF (1 MB) | Supplemental
  • 744 Views
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Article
Capturing state-dependent dynamic events of GABAA-receptors: a microscopic look into the structural and functional insights
Pavan V. Payghan, Indrani Bera, Dhananjay Bhattacharyya & Nanda Ghoshal
Pages: 1818-1837
Published online: 12 Jan 2016
AbstractforCapturing state-dependent dynamic events of GABAA-receptors: a microscopic look into the structural and functional insights | Full Text | References | PDF (2 MB) | Supplemental
  • 278 Views
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