Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 1 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 1 (2020)

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Research Articles

Article
Insights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300
Zhengfei Yu, Ye Liu, Jingxuan Zhu, Jiarui Han, Xiaopian Tian, Weiwei Han & Li Zhao
Pages: 1-12
Published online: 04 Mar 2019
AbstractforInsights from molecular dynamics simulations and steered molecular dynamics simulations to exploit new trends of the interaction between HIF-1α and p300 | Full Text | References | PDF (3.2 MB) | EPUB
  • 557 Views
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Article
Identification of Pak1 inhibitors using water thermodynamic analysis
Jayashree Biswal, Prajisha Jayaprakash, Rayala Suresh Kumar, Ganesh Venkatraman, Saritha Poopandi, Raghu Rangasamy & Jeyakanthan Jeyaraman
Pages: 13-31
Published online: 17 Feb 2019
AbstractforIdentification of Pak1 inhibitors using water thermodynamic analysis | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 211 Views
  • 9 CrossRef citations
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Article
Negative allosteric modulators of cannabinoid receptor 2: protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist
Pankaj Pandey, Kuldeep K. Roy & Robert J. Doerksen
Pages: 32-47
Published online: 05 Feb 2019
AbstractforNegative allosteric modulators of cannabinoid receptor 2: protein modeling, binding site identification and molecular dynamics simulations in the presence of an orthosteric agonist | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 1112 Views
  • 23 CrossRef citations
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Article
An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies
Kriti Kashyap & Rita Kakkar
Pages: 48-65
Published online: 07 Feb 2019
AbstractforAn insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 441 Views
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Article
Good and bad molecular fingerprints for human rhinovirus 3C protease inhibition: identification, validation, and application in designing of new inhibitors through Monte Carlo-based QSAR study
Sanskar Jain, Sk. Abdul Amin, Nilanjan Adhikari, Tarun Jha & Shovanlal Gayen
Pages: 66-77
Published online: 31 Jan 2019
AbstractforGood and bad molecular fingerprints for human rhinovirus 3C protease inhibition: identification, validation, and application in designing of new inhibitors through Monte Carlo-based QSAR study | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 260 Views
  • 31 CrossRef citations
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Article
Spermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies
Sakineh Sadeghi-Kaji, Behzad Shareghi, Ali Akbar Saboury & Sadegh Farhadian
Pages: 78-88
Published online: 27 Feb 2019
AbstractforSpermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies | Full Text | References | PDF (1.8 MB) | EPUB
  • 182 Views
  • 9 CrossRef citations
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Article
How does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study
Hao Zhang, Xinheng He, Duan Ni, Linkai Mou, Xiangyu Chen & Shaoyong Lu
Pages: 89-100
Published online: 05 Feb 2019
AbstractforHow does the novel T315L mutation of breakpoint cluster region-abelson (BCR-ABL) kinase confer resistance to ponatinib: a comparative molecular dynamics simulation study | Full Text | References | PDF (2.2 MB) | EPUB
  • 658 Views
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Article
Spermine as a possible endogenous allosteric activator of carboxypeptidase A: multispectroscopic and molecular simulation studies
Mozhgan Mohammadi, Behzad Shareghi, Ali Akbar Saboury & Sadegh Farhadian
Pages: 101-113
Published online: 14 Feb 2019
AbstractforSpermine as a possible endogenous allosteric activator of carboxypeptidase A: multispectroscopic and molecular simulation studies | Full Text | References | PDF (2.4 MB) | EPUB
  • 181 Views
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Article
Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans
Dhirendra Kumar Sharma, Mohammad Quadir Siddiqui, Nikhil Gadewal, Rajan Kumar Choudhary, Ashok Kumar Varma, Hari Sharan Misra & Yogendra Singh Rajpurohit
Pages: 114-123
Published online: 10 Feb 2019
AbstractforPhosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 218 Views
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Article
In silico identification of mimicking molecule(s) triggering von Willebrand factor in human: a molecular drug target for regulating coagulation pathway
Garima Rana, Rajesh Kumar Pathak, Rohit Shukla & Mamta Baunthiyal
Pages: 124-136
Published online: 10 Feb 2019
AbstractforIn silico identification of mimicking molecule(s) triggering von Willebrand factor in human: a molecular drug target for regulating coagulation pathway | Full Text | References | PDF (2.8 MB) | EPUB
  • 242 Views
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Article
Insights into the structure–function relationship of both wild and mutant zinc transporter ZnT8 in human: a computational structural biology approach
Manoj Kumar Gupta & Ramakrishna Vadde
Pages: 137-151
Published online: 31 Jan 2019
AbstractforInsights into the structure–function relationship of both wild and mutant zinc transporter ZnT8 in human: a computational structural biology approach | Full Text | References | PDF (3.3 MB) | EPUB
  • 414 Views
  • 15 CrossRef citations
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Article
On the early events of the calcium-induced activation of coagulation factor XIII-A2 and tissue transglutaminase: an in silico study
Attila Fekete, István Komáromi & Dániel Mucs
Pages: 152-167
Published online: 17 Feb 2019
AbstractforOn the early events of the calcium-induced activation of coagulation factor XIII-A2 and tissue transglutaminase: an in silico study | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 357 Views
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Article
2D- and 3D-QSAR modelling, molecular docking and in vitro evaluation studies on 18β-glycyrrhetinic acid derivatives against triple-negative breast cancer cell line
Aparna Shukla, Rekha Tyagi, Sanjeev Meena, Dipak Datta, Santosh Kumar Srivastava & Feroz Khan
Pages: 168-185
Published online: 22 Feb 2019
Abstractfor2D- and 3D-QSAR modelling, molecular docking and in vitro evaluation studies on 18β-glycyrrhetinic acid derivatives against triple-negative breast cancer cell line | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 665 Views
  • 23 CrossRef citations
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Article
Comparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach
Nikhil Maroli & Ponmalai Kolandaivel
Pages: 186-199
Published online: 10 Feb 2019
AbstractforComparative study of stability and transport of molecules through cyclic peptide nanotube and aquaporin: a molecular dynamics simulation approach | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 393 Views
  • 13 CrossRef citations
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Article
Chloro and bromo-pyrazole curcumin Knoevenagel condensates augmented anticancer activity against human cervical cancer cells: design, synthesis, in silico docking and in vitro cytotoxicity analysis
Monika Chaudhary, Neeraj Kumar, Ashish Baldi, Ramesh Chandra, M. Arockia Babu & Jitender Madan
Pages: 200-218
Published online: 27 Feb 2019
AbstractforChloro and bromo-pyrazole curcumin Knoevenagel condensates augmented anticancer activity against human cervical cancer cells: design, synthesis, in silico docking and in vitro cytotoxicity analysis | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 602 Views
  • 30 CrossRef citations
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Article
Evaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations
Kalaiarasi Chinnasamy, Manjula Saravanan & Kumaradhas Poomani
Pages: 219-235
Published online: 30 Apr 2019
AbstractforEvaluation of binding and antagonism/downregulation of brilanestrant molecule in estrogen receptor-α via quantum mechanics/molecular mechanics, molecular dynamics and binding free energy calculations | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 190 Views
  • 8 CrossRef citations
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Article
A novel cadmium(II) complex of bipyridine derivative: synthesis, X-ray crystal structure, DNA-binding and antibacterial activities
Tahere Kondori, Niloufar Akbarzadeh-T, Khatereh Abdi, Michal Dušek & Václav Eigner
Pages: 236-247
Published online: 19 Feb 2019
AbstractforA novel cadmium(II) complex of bipyridine derivative: synthesis, X-ray crystal structure, DNA-binding and antibacterial activities | Full Text | References | PDF (1.7 MB) | EPUB
  • 231 Views
  • 17 CrossRef citations
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Article
Virtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer’s disease
Rohit Shukla & Tiratha Raj Singh
Pages: 248-262
Published online: 21 Feb 2019
AbstractforVirtual screening, pharmacokinetics, molecular dynamics and binding free energy analysis for small natural molecules against cyclin-dependent kinase 5 for Alzheimer’s disease | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 625 Views
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Letters to the Editor

Letter
Indole fragments for the design of lead molecules against pancreatitis
K. V. Dileep, S. Ashok, C. Remya, K. Y. Dharmendra, Horacio Pérez-Sánchez & C. Sadasivan
Pages: 263-267
Published online: 19 Feb 2019
AbstractforIndole fragments for the design of lead molecules against pancreatitis | Full Text | References | PDF (844.7 KB) | EPUB | Supplemental
  • 107 Views
  • 1 CrossRef citations
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Letter
Systematic analysis of NO Regular Secondary structural regions (NORS) in membrane and non-membrane proteins
Konda Mani Saravanan, Yin Peng & Yanjie Wei
Pages: 268-274
Published online: 05 Feb 2019
First Page PreviewforSystematic analysis of NO Regular Secondary structural regions (NORS) in membrane and non-membrane proteins | Full Text | References | PDF (1.1 MB) | EPUB
  • 185 Views
  • 3 CrossRef citations
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Letter
Binding, selectivity and sequence recognition of matrix metalloproteinase-2 to oligopeptides
Cai Yao, Binbin Chen, Zhengzhong Kang, Yingchun Liu, Xianrong Qi & Qi Wang
Pages: 275-282
Published online: 21 Feb 2019
AbstractforBinding, selectivity and sequence recognition of matrix metalloproteinase-2 to oligopeptides | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 187 Views
  • 4 CrossRef citations
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Letter
New water-soluble Fe3O4@SiO2 magnetic nanoparticles functionalized with levetiracetam drug for adsorption of essential biomolecules by case studies of DNA and HSA
Nahid Shahabadi, Saba Hadidi & Farshad Shiri
Pages: 283-294
Published online: 19 Feb 2019
AbstractforNew water-soluble Fe3O4@SiO2 magnetic nanoparticles functionalized with levetiracetam drug for adsorption of essential biomolecules by case studies of DNA and HSA | Full Text | References | PDF (2.4 MB) | EPUB
  • 207 Views
  • 14 CrossRef citations
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Letter
A paradigm towards the antimalarial quest: in silico identification and biological evaluation of novel inhibitors targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase
Drista Sharma, Ravikrishna Dada, Kiran Kumar Tejavath, Praveen Rai, Rani Soni, Srinivasarao Yaragorla & Tarun Kumar Bhatt
Pages: 295-301
Published online: 10 Feb 2019
First Page PreviewforA paradigm towards the antimalarial quest: in silico identification and biological evaluation of novel inhibitors targeting 1-deoxy-D-xylulose-5-phosphate reductoisomerase | Full Text | References | PDF (1.6 MB) | EPUB
  • 130 Views
  • 1 CrossRef citations
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Letter
Effect of tea catechins on tRNA structure and dynamics
P. Chanphai & H. A. Tajmir-Riahi
Pages: 302-306
Published online: 10 Feb 2019
AbstractforEffect of tea catechins on tRNA structure and dynamics | Full Text | References | PDF (1.1 MB) | EPUB
  • 86 Views
  • 3 CrossRef citations
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Letter
DNA binding and cleavage, cytotoxicity and antimicrobial studies of Co(II), Ni(II), Cu(II) and Zn(II) complexes of 1-((E)-(4-(trifluoromethoxy)phenylimino)methyl)naphthalen-2-ol Schiff base
Aveli Rambabu, Marri Pradeep Kumar, Nirmala Ganji, Sreenu Daravath & Shivaraj
Pages: 307-316
Published online: 14 Feb 2019
First Page PreviewforDNA binding and cleavage, cytotoxicity and antimicrobial studies of Co(II), Ni(II), Cu(II) and Zn(II) complexes of 1-((E)-(4-(trifluoromethoxy)phenylimino)methyl)naphthalen-2-ol Schiff base | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 306 Views
  • 35 CrossRef citations
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