Journal of Biomolecular Structure and Dynamics, Volume 33, Issue 11 (2015)

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Journal of Biomolecular Structure and Dynamics, Volume 33, Issue 11 (2015)

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Articles

Article
How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches?
Ol’ha O. Brovarets’ & Dmytro M. Hovorun
Pages: 2297-2315
Published online: 23 Jun 2015
AbstractforHow many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches? | Full Text | References | PDF (1.4 MB) | Supplemental
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Article
Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles
Malihe Ebrahimi, Taghi Khayamian, Hassan Hadadzadeh, Badraldin Ebrahim Sayed Tabatabaei, Zahra Jannesari & Ghazale Khaksar
Pages: 2316-2329
Published online: 11 Feb 2015
AbstractforSpectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles | Full Text | References | PDF (793.5 KB) | Supplemental
  • 521 Views
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Article
Molecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes
Pratim Chakraborti, Rachana Banerjee, Ayan Roy, Sunanda Mandal & Subhasish Mukhopadhyay
Pages: 2330-2346
Published online: 07 Aug 2015
AbstractforMolecular characterization influencing metal resistance in the Cupriavidus/Ralstonia genomes | Full Text | References | PDF (1.6 MB) | Supplemental
  • 210 Views
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Article
Improvement of Cd2+ uptake ability of SmtA protein by Lys/Cys mutation; experimental and theoretical studies
B. Saffar, A. Mehri Ghahfarrokhi, K. Mahnam & M. Mobini-Dehkordi
Pages: 2347-2359
Published online: 19 Jun 2015
AbstractforImprovement of Cd2+ uptake ability of SmtA protein by Lys/Cys mutation; experimental and theoretical studies | Full Text | References | PDF (753 KB) | Supplemental
  • 219 Views
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Article
Investigation of ligand selectivity in CYP3A7 by molecular dynamics simulations
Jing-Rong Fan, Qing-Chuan Zheng, Ying-Lu Cui, Wei-Kang Li & Hong-Xing Zhang
Pages: 2360-2367
Published online: 23 Jun 2015
AbstractforInvestigation of ligand selectivity in CYP3A7 by molecular dynamics simulations | Full Text | References | PDF (685.8 KB) | Supplemental
  • 485 Views
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Article
Inhibition of Janus kinases by tyrosine phosphorylation inhibitor, Tyrphostin AG-490
Sajid Rashid, Nousheen Bibi, Zahida Parveen & Shagufta Shafique
Pages: 2368-2379
Published online: 23 Jun 2015
AbstractforInhibition of Janus kinases by tyrosine phosphorylation inhibitor, Tyrphostin AG-490 | Full Text | References | PDF (840.1 KB) | Supplemental
  • 460 Views
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Article
In silico deletion of PtsG gene in Escherichia coli genome-scale model predicts increased succinate production from glycerol
Bashir Sajo Mienda & Mohd Shahir Shamsir
Pages: 2380-2389
Published online: 08 Jun 2015
AbstractforIn silico deletion of PtsG gene in Escherichia coli genome-scale model predicts increased succinate production from glycerol | Full Text | References | PDF (282.1 KB)
  • 437 Views
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Article
Kinetic simulation of malate-aspartate and citrate-pyruvate shuttles in association with Krebs cycle
Kalyani Korla, Lakshmipathi Vadlakonda & Chanchal K. Mitra
Pages: 2390-2403
Published online: 11 Feb 2015
AbstractforKinetic simulation of malate-aspartate and citrate-pyruvate shuttles in association with Krebs cycle | Full Text | References | PDF (1.8 MB)
  • 650 Views
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Article
Identification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies
Bhavik Sawhney, Kriti Chopra, Rohan Misra & Akash Ranjan
Pages: 2404-2420
Published online: 17 Jul 2015
AbstractforIdentification of Plasmodium falciparum apicoplast-targeted tRNA-guanine transglycosylase and its potential inhibitors using comparative genomics, molecular modelling, docking and simulation studies | Full Text | References | PDF (1,018.9 KB) | Supplemental
  • 420 Views
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Article
Exploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 of Plasmodium falciparum: a docking and simulation study
Saurabh Gupta, Alka Jadaun, Himansu Kumar, Utkarsh Raj, Pritish Kumar Varadwaj & A.R. Rao
Pages: 2421-2441
Published online: 15 Jun 2015
AbstractforExploration of new drug-like inhibitors for serine/threonine protein phosphatase 5 of Plasmodium falciparum: a docking and simulation study | Full Text | References | PDF (1.3 MB)
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Article
Human furin Cys198 imposes dihedral and positional restraints on His194 for optimal Ser386-proton transfer
Olaposi I. Omotuyi & Tsuyoshi Hamada
Pages: 2442-2451
Published online: 16 Jun 2015
AbstractforHuman furin Cys198 imposes dihedral and positional restraints on His194 for optimal Ser386-proton transfer | Full Text | References | PDF (836.1 KB)
  • 217 Views
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Article
Pocket analysis of the full-length cholix toxin. An assessment of the structure–dynamics of the apo catalytic domain
Miguel R. Lugo & A. Rod Merrill
Pages: 2452-2468
Published online: 23 Jan 2015
AbstractforPocket analysis of the full-length cholix toxin. An assessment of the structure–dynamics of the apo catalytic domain | Full Text | References | PDF (1 MB) | Supplemental
  • 174 Views
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Article
Functional assessment of intrinsic disorder central domains of BRCA1
Lumbini R. Yadav, Sharad Rai, M.V. Hosur & Ashok K. Varma
Pages: 2469-2478
Published online: 23 Jan 2015
AbstractforFunctional assessment of intrinsic disorder central domains of BRCA1 | Full Text | References | PDF (414 KB)
  • 366 Views
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Article
A method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis
You Zhou, Ning Zhang, Bi-Qing Li, Tao Huang, Yu-Dong Cai & Xiang-Yin Kong
Pages: 2479-2490
Published online: 23 Jan 2015
AbstractforA method to distinguish between lysine acetylation and lysine ubiquitination with feature selection and analysis | Full Text | References | PDF (536.5 KB) | Supplemental
  • 373 Views
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Article
In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study
Changdev G. Gadhe, Anand Balupuri & Seung Joo Cho
Pages: 2491-2510
Published online: 23 Jan 2015
AbstractforIn silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study | Full Text | References | PDF (1.3 MB) | Supplemental
  • 611 Views
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Article
Molecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I
D. Benrezkallah, M. Dauchez & A.M. Krallafa
Pages: 2511-2521
Published online: 03 Feb 2015
AbstractforMolecular dynamics of the salt dependence of a cold-adapted enzyme: endonuclease I | Full Text | References | PDF (866.2 KB)
  • 255 Views
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Article
Simulating the antimicrobial mechanism of human β-defensin-3 with coarse-grained molecular dynamics
Xi Zhao, Hui Yu, Liu Yang, Qianqian Li & Xuri Huang
Pages: 2522-2529
Published online: 23 Jan 2015
AbstractforSimulating the antimicrobial mechanism of human β-defensin-3 with coarse-grained molecular dynamics | Full Text | References | PDF (706.2 KB)
  • 330 Views
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