Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 7 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 7 (2020)

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Research Articles

Article
Homology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III
Saroj Kumar Panda, Shalini Saxena & Lalitha Guruprasad
Pages: 1887-1902
Published online: 08 Jun 2019
AbstractforHomology modeling, docking and structure-based virtual screening for new inhibitor identification of Klebsiella pneumoniae heptosyltransferase-III | Full Text | References | PDF (6.1 MB) | EPUB
  • 366 Views
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Article
Discovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics
Maharajan Sivakumar, Kandasamy Saravanan, Velautham Saravanan, Srinivasan Sugarthi, Shankar Madan kumar, Mustafa Alhaji Isa, Perumal Rajakumar & Sanmargam Aravindhan
Pages: 1903-1917
Published online: 30 May 2019
AbstractforDiscovery of new potential triplet acting inhibitor for Alzheimer’s disease via X-ray crystallography, molecular docking and molecular dynamics | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 282 Views
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Article
Bindings of PPARγ ligand-binding domain with 5-cholesten-3β, 25-diol, 3-sulfate: accurate prediction by molecular simulation
Zhiwei Yang, Yizhen Zhao, Dongxiao Hao, Shunlin Ren, Xiaohui Yuan, Lingjie Meng & Shengli Zhang
Pages: 1918-1926
Published online: 22 May 2019
AbstractforBindings of PPARγ ligand-binding domain with 5-cholesten-3β, 25-diol, 3-sulfate: accurate prediction by molecular simulation | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 270 Views
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Article
Unraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach
Shreya Dubey, Suneel Kumar Madana, Monika Kallubai, Arijit Sarkar & Rajagopal Subramanyam
Pages: 1927-1937
Published online: 30 May 2019
AbstractforUnraveling the stability of plasma proteins upon interaction of synthesized uridine products: biophysical and molecular dynamics approach | Full Text | References | PDF (2.8 MB) | EPUB
  • 123 Views
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Article
Insights into resistance mechanism of hepatitis C virus nonstructural 3/4A protease mutant to boceprevir using umbrella sampling simulation study
Esmaeil Behmard & Ebrahim Barzegari
Pages: 1938-1945
Published online: 31 May 2019
AbstractforInsights into resistance mechanism of hepatitis C virus nonstructural 3/4A protease mutant to boceprevir using umbrella sampling simulation study | Full Text | References | PDF (1.9 MB) | EPUB
  • 110 Views
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Article
Unprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell
Pei Guo & Sik Lok Lam
Pages: 1946-1953
Published online: 30 May 2019
AbstractforUnprecedented hydrophobic stabilizations from a reverse wobble T·T mispair in DNA minidumbbell | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 154 Views
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Article
In silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer
Encieh Delshad, Fatemeh T. Shamsabadi, Shabbou Bahramian, Fatemeh Mehravar, Hossein Maghsoudi & Mohammad Shafiee
Pages: 1954-1962
Published online: 08 Jun 2019
AbstractforIn silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer | Full Text | References | PDF (1.8 MB) | EPUB
  • 156 Views
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Articles

Article
Computational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway
Vijay Bhardwaj & Rituraj Purohit
Pages: 1963-1974
Published online: 30 May 2019
AbstractforComputational investigation on effect of mutations in PCNA resulting in structural perturbations and inhibition of mismatch repair pathway | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 355 Views
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Research Articles

Article
The four repeat Giardia lamblia telomere forms tetramolecular G-quadruplex with antiparallel topology
Aparna Bansal & Shrikant Kukreti
Pages: 1975-1983
Published online: 06 Jun 2019
AbstractforThe four repeat Giardia lamblia telomere forms tetramolecular G-quadruplex with antiparallel topology | Full Text | References | PDF (1.2 MB) | EPUB
  • 135 Views
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Article
Preferential recognition of epitopes on peroxynitrite-modified alpha-2-macroglobulin by circulating autoantibodies in rheumatoid arthritis patients
Heena Imtiaz Malik, Abdul Rouf Mir, Minhal Abidi, Safia Habib, Fahim Halim Khan & Moinuddin
Pages: 1984-1994
Published online: 08 Jun 2019
AbstractforPreferential recognition of epitopes on peroxynitrite-modified alpha-2-macroglobulin by circulating autoantibodies in rheumatoid arthritis patients | Full Text | References | PDF (1.3 MB) | EPUB
  • 91 Views
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Article
Computational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells
Arun John, Muthukumaran Sivashanmugam, Sulochana Konerirajapuram Natarajan & Vetrivel Umashankar
Pages: 1995-2006
Published online: 30 May 2019
AbstractforComputational modeling of novel inhibitory peptides targeting proteoglycan like region of carbonic anhydrase IX and in vitro validation in HeLa cells | Full Text | References | PDF (3 MB) | EPUB
  • 275 Views
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Article
Structure and dynamics analysis of a new member heparinase II/III of family 12 polysaccharide lyase from Pseudopedobacter saltans by computational modeling and small-angle X-ray scattering
Karthika Balasubramaniam, Kedar Sharma & Arun Goyal
Pages: 2007-2020
Published online: 03 Jun 2019
AbstractforStructure and dynamics analysis of a new member heparinase II/III of family 12 polysaccharide lyase from Pseudopedobacter saltans by computational modeling and small-angle X-ray scattering | Full Text | References | PDF (4.7 MB) | EPUB
  • 296 Views
  • 2 CrossRef citations
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Article
The inhibitory kinetics and mechanism of glycolic acid on lipase
Tian-Tian Liu, Wei-Chao Su, Qing-Xi Chen, Dong-Yan Shen & Jiang-Xing Zhuang
Pages: 2021-2028
Published online: 05 Aug 2019
AbstractforThe inhibitory kinetics and mechanism of glycolic acid on lipase | Full Text | References | PDF (1.3 MB) | EPUB
  • 335 Views
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Article
Groove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies
Guowen Zhang, Zhisheng Zhou, Jianjian Xu, Yijing Liao & Xing Hu
Pages: 2029-2037
Published online: 03 Jun 2019
AbstractforGroove binding between ferulic acid and calf thymus DNA: spectroscopic methodology combined with chemometrics and molecular docking studies | Full Text | References | PDF (1.6 MB) | EPUB
  • 220 Views
  • 3 CrossRef citations
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Article
Molecular interactions of MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin
Ayonbala Baral, Lakkoji Satish, Dipti Prakasini Das, Harekrushna Sahoo & Malay Kumar Ghosh
Pages: 2038-2046
Published online: 13 Jul 2019
AbstractforMolecular interactions of MnO2@RGO (manganese dioxide-reduced graphene oxide) nanocomposites with bovine serum albumin | Full Text | References | PDF (1.5 MB) | EPUB
  • 256 Views
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Article
Studying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior
Rafael F. Soares, Deborah Antunes, Lucianna H. S. Santos, Gisele Vieira Rocha, Leonardo Soares Bastos, Ana Carolina R. Guimarães & Ernesto R. Caffarena
Pages: 2047-2056
Published online: 11 Jun 2019
AbstractforStudying effects of different protonation states of His11 and His102 in ribose-5-phosphate isomerase of Trypanosoma cruzi: an example of cooperative behavior | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 166 Views
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Article
Impacts of hydrophobicity and ionicity of phendione-based cobalt(II)/(III) complexes on binding with bovine serum albumin
Selvan Nehru, John Abraham Anitha Priya, Sekar Hariharan, Rajadurai Vijay Solomon & Selvakumar Veeralakshmi
Pages: 2057-2067
Published online: 30 May 2019
AbstractforImpacts of hydrophobicity and ionicity of phendione-based cobalt(II)/(III) complexes on binding with bovine serum albumin | Full Text | References | PDF (2.5 MB) | EPUB
  • 208 Views
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Article
S100A4: a novel partner for heat shock protein 47 in antler stem cells and insight into the calcium ion-induced conformational changes
Yudong Shang, Zhengyao Zhang, Hengxing Ba, Datao Wang, Xiaoyan Qi & Chunyi Li
Pages: 2068-2079
Published online: 17 Jun 2019
AbstractforS100A4: a novel partner for heat shock protein 47 in antler stem cells and insight into the calcium ion-induced conformational changes | Full Text | References | PDF (3.5 MB) | EPUB
  • 269 Views
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Article
An integrated in silico approach to understand protein–protein interactions: human meprin-β with fetuin-A
Yuthika Dholey, Ankur Chaudhuri & Sibani Sen Chakraborty
Pages: 2080-2092
Published online: 11 Jun 2019
AbstractforAn integrated in silico approach to understand protein–protein interactions: human meprin-β with fetuin-A | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 249 Views
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Article
In silico based unraveling of New Delhi metallo-β-lactamase (NDM-1) inhibitors from natural compounds: a molecular docking and molecular dynamics simulation study
Mashihur Rahman & Md. Khurshid Alam Khan
Pages: 2093-2103
Published online: 11 Jun 2019
AbstractforIn silico based unraveling of New Delhi metallo-β-lactamase (NDM-1) inhibitors from natural compounds: a molecular docking and molecular dynamics simulation study | Full Text | References | PDF (2.5 MB) | EPUB
  • 460 Views
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Article
Structural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy
İrem Yılmaz, Özkan Yıldız & Filiz Korkmaz
Pages: 2104-2115
Published online: 03 Jun 2019
AbstractforStructural properties of an engineered outer membrane protein G mutant, OmpG-16SL, investigated with infrared spectroscopy | Full Text | References | PDF (2.5 MB) | EPUB
  • 143 Views
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Article
Mechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach
Vitor Won-Held Rabelo, Nelilma Correia Romeiro, Izabel Christina Nunes de Palmer Paixão & Paula Alvarez Abreu
Pages: 2116-2127
Published online: 13 Jun 2019
AbstractforMechanism of resistance to acyclovir in thymidine kinase mutants from Herpes simplex virus type 1: a computational approach | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 384 Views
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Article
Studies on the interaction between HSA and new halogenated metformin derivatives: influence of lipophilic groups in the binding ability
Otávio Augusto Chaves, Bijo Mathew, Della Grace Thomas Parambi, Cosme Henrique C. S. de Oliveira, Dari Cesarin-Sobrinho, Balasubramanian Lakshminarayanan, Sadiya Najeeb, E. K. Nafna, Akash Marathakam, Md. Sahab Uddin, Monu Joy & José Carlos Netto-Ferreira
Pages: 2128-2140
Published online: 11 Jun 2019
AbstractforStudies on the interaction between HSA and new halogenated metformin derivatives: influence of lipophilic groups in the binding ability | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 280 Views
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Article
Binding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies
Jianzhong chen, Baohua Yin, Laixue Pang, Wei Wang, John Z. H. Zhang & Tong Zhu
Pages: 2141-2155
Published online: 14 Jun 2019
AbstractforBinding modes and conformational changes of FK506-binding protein 51 induced by inhibitor bindings: insight into molecular mechanisms based on multiple simulation technologies | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 308 Views
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Article
Identification of potential tumour-associated carbonic anhydrase isozyme IX inhibitors: atom-based 3D-QSAR modelling, pharmacophore-based virtual screening and molecular docking studies
Avinash Kumar, Ekta Rathi & Suvarna G. Kini
Pages: 2156-2170
Published online: 08 Jun 2019
AbstractforIdentification of potential tumour-associated carbonic anhydrase isozyme IX inhibitors: atom-based 3D-QSAR modelling, pharmacophore-based virtual screening and molecular docking studies | Full Text | References | PDF (2.7 MB) | EPUB
  • 354 Views
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Review Article

Review Article
Mammalian cystatin and protagonists in brain diseases
Fakhra Amin, Mohd Shahnawaz Khan & Bilqees Bano
Pages: 2171-2196
Published online: 05 Jun 2019
AbstractforMammalian cystatin and protagonists in brain diseases | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 866 Views
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Letter to the Editor

Letter
Spectral and molecular docking studies on the interaction of three flavonoids with bovine serum albumin
Shuyun Bi, Jun Wu, Xiaoyue Sun, Rui Zhao, Di Shao & Xu Li
Pages: 2197-2205
Published online: 03 Jun 2019
AbstractforSpectral and molecular docking studies on the interaction of three flavonoids with bovine serum albumin | Full Text | References | PDF (2.4 MB) | EPUB
  • 204 Views
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