Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 11 (2016)

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Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 11 (2016)

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Research Articles

Article
Model-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources
Bashir Sajo Mienda, Mohd Shahir Shamsir & Rosli Md. Illias
Pages: 2305-2316
Published online: 06 Jan 2016
AbstractforModel-assisted formate dehydrogenase-O (fdoH) gene knockout for enhanced succinate production in Escherichia coli from glucose and glycerol carbon sources | Full Text | References | PDF (313.2 KB)
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Article
Zinc-induced heterodimer formation between metal-binding domains of intact and naturally modified amyloid-beta species: implication to amyloid seeding in Alzheimer’s disease?
Yuri V. Mezentsev, Alexei E. Medvedev, Olga I. Kechko, Alexander A. Makarov, Alexis S. Ivanov, Alexey B. Mantsyzov & Sergey A. Kozin
Pages: 2317-2326
Published online: 21 Mar 2016
AbstractforZinc-induced heterodimer formation between metal-binding domains of intact and naturally modified amyloid-beta species: implication to amyloid seeding in Alzheimer’s disease? | Full Text | References | PDF (399.9 KB) | Supplemental
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Article
Deciphering structure-activity relationships in a series of Tat/TAR inhibitors
Lise Pascale, Alejandro López González, Audrey Di Giorgio, Marc Gaysinski, Jordi Teixido Closa, Roger Estrada Tejedor, Stéphane Azoulay & Nadia Patino
Pages: 2327-2338
Published online: 06 Jan 2016
AbstractforDeciphering structure-activity relationships in a series of Tat/TAR inhibitors | Full Text | References | PDF (662.2 KB) | Supplemental
  • 165 Views
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Article
2-Deoxyglucose conjugated platinum (II) complexes for targeted therapy: design, synthesis, and antitumor activity
Qian Mi, Yuru Ma, Xiangqian Gao, Ran Liu, Pengxing Liu, Yi Mi, Xuegang Fu & Qingzhi Gao
Pages: 2339-2350
Published online: 30 Nov 2015
Abstractfor2-Deoxyglucose conjugated platinum (II) complexes for targeted therapy: design, synthesis, and antitumor activity | Full Text | References | PDF (753 KB)
  • 504 Views
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Article
Exploring the interaction between human focal adhesion kinase and inhibitors: a molecular dynamic simulation and free energy calculations
Jiu-Yu Zhan, Ji-Long Zhang, Yan Wang, Ye Li, Hong-Xing Zhang & Qing-Chuan Zheng
Pages: 2351-2366
Published online: 04 Mar 2016
AbstractforExploring the interaction between human focal adhesion kinase and inhibitors: a molecular dynamic simulation and free energy calculations | Full Text | References | PDF (1.2 MB)
  • 186 Views
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Article
Molecular docking and structure-based virtual screening studies of potential drug target, CAAX prenyl proteases, of Leishmania donovani
Shalini Singh, Sitrarasu Vijaya Prabhu, Venkatesan Suryanarayanan, Ruchika Bhardwaj, Sanjeev Kumar Singh & Vikash Kumar Dubey
Pages: 2367-2386
Published online: 06 Jan 2016
AbstractforMolecular docking and structure-based virtual screening studies of potential drug target, CAAX prenyl proteases, of Leishmania donovani | Full Text | References | PDF (1.7 MB) | Supplemental
  • 630 Views
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Article
Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations
Begum Alaybeyoglu, Berna Sariyar Akbulut & Elif Ozkirimli
Pages: 2387-2398
Published online: 17 Mar 2016
AbstractforInsights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations | Full Text | References | PDF (554.1 KB) | Supplemental
  • 457 Views
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Article
A comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis
Zeynab Fakhar, Suhashni Naiker, Claudio N. Alves, Thavendran Govender, Glenn E.M. Maguire, Jeronimo Lameira, Gyanu Lamichhane, Hendrik G. Kruger & Bahareh Honarparvar
Pages: 2399-2417
Published online: 04 Apr 2016
AbstractforA comparative modeling and molecular docking study on Mycobacterium tuberculosis targets involved in peptidoglycan biosynthesis | Full Text | References | PDF (1.3 MB) | Supplemental
  • 516 Views
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Article
Dual anti-inflammatory and selective inhibition mechanism of leukotriene A4 hydrolase/aminopeptidase: insights from comparative molecular dynamics and binding free energy analyses
Patrick Appiah-Kubi & Mahmoud E.S. Soliman
Pages: 2418-2433
Published online: 11 Jan 2016
AbstractforDual anti-inflammatory and selective inhibition mechanism of leukotriene A4 hydrolase/aminopeptidase: insights from comparative molecular dynamics and binding free energy analyses | Full Text | References | PDF (1.6 MB) | Supplemental
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Article
Molecular dynamics-based investigation of InhA substrate binding loop for diverse biological activity of direct InhA inhibitors
Vivek Kumar & M. Elizabeth Sobhia
Pages: 2434-2452
Published online: 20 May 2016
AbstractforMolecular dynamics-based investigation of InhA substrate binding loop for diverse biological activity of direct InhA inhibitors | Full Text | References | PDF (1.4 MB)
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Article
Docking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase
Aramice Y.S. Malkhasian & Brendan J. Howlin
Pages: 2453-2461
Published online: 02 Feb 2016
AbstractforDocking and DFT studies on ligand binding to Quercetin 2,3-dioxygenase | Full Text | References | PDF (1 MB)
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Article
Mutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding
Ramin Ekhteiari Salmas, Mert Mestanoglu, Ayhan Unlu, Mine Yurtsever & Serdar Durdagi
Pages: 2462-2468
Published online: 02 Feb 2016
AbstractforMutated form (G52E) of inactive diphtheria toxin CRM197: molecular simulations clearly display effect of the mutation to NAD binding | Full Text | References | PDF (523.1 KB) | Supplemental
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Review Articles

Article
Allostery in BAX protein activation
Zhenyan Jiang, Hansi Zhang & Rainer A. Böckmann
Pages: 2469-2480
Published online: 06 Feb 2016
AbstractforAllostery in BAX protein activation | Full Text | References | PDF (1.3 MB)
  • 270 Views
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Research Articles

Article
A combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors
Naga Srinivas Tripuraneni & Mohammed Afzal Azam
Pages: 2481-2492
Published online: 12 Apr 2016
AbstractforA combination of pharmacophore modeling, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on PDE4 enzyme inhibitors | Full Text | References | PDF (555.8 KB) | Supplemental
  • 410 Views
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Article
Destructive effect of anticancer oxali-palladium on heme degradation through the generation of endogenous hydrogen peroxide
K. Abbasi-Tajarag, A. Divsalar, A.A. Saboury, B. Ghalandari & H. Ghourchian
Pages: 2493-2504
Published online: 25 Apr 2016
AbstractforDestructive effect of anticancer oxali-palladium on heme degradation through the generation of endogenous hydrogen peroxide | Full Text | References | PDF (591.4 KB)
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Article
Design and evaluation of an apta-nano-sensor to detect Acetamiprid in vitro and in silico
Mahmoud Jokar, Mohammad Hassan Safaralizadeh, Farzin Hadizadeh, Fatemeh Rahmani & Mohammad Reza Kalani
Pages: 2505-2517
Published online: 17 Feb 2016
AbstractforDesign and evaluation of an apta-nano-sensor to detect Acetamiprid in vitro and in silico | Full Text | References | PDF (3.3 MB) | Supplemental
  • 498 Views
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Article
Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA
Bhumika Ray, Shweta Agarwal, Neelam Lohani, Moganty R. Rajeswari & Ranjana Mehrotra
Pages: 2518-2535
Published online: 17 Feb 2016
AbstractforStructural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA | Full Text | References | PDF (494.6 KB)
  • 264 Views
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