Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 3 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 3 (2020)

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Research Articles

Article
Connecting the dots in the mechanism of action of Cucurbitacin E (CurE) – path analysis and steered molecular dynamics reveal the precise site of entry and the passage of CurE in filamentous actin
L. Roopa, P. S. Akshai & R. Pravin Kumar
Pages: 635-646
Published online: 27 Mar 2019
AbstractforConnecting the dots in the mechanism of action of Cucurbitacin E (CurE) – path analysis and steered molecular dynamics reveal the precise site of entry and the passage of CurE in filamentous actin | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 149 Views
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Article
Local structural unfolding at the edge-strands of beta sheets is the molecular basis for instability and aggregation of G85R and G93A mutants of superoxide dismutase 1
Debasish Kumar Ghosh, Akshaykumar Nanaji Shrikondawar & Akash Ranjan
Pages: 647-659
Published online: 11 Mar 2019
AbstractforLocal structural unfolding at the edge-strands of beta sheets is the molecular basis for instability and aggregation of G85R and G93A mutants of superoxide dismutase 1 | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 402 Views
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Article
Identification of repurposed protein kinase B binders from FDA-approved drug library: a hybrid–structure activity relationship and systems modeling based approach
Om Prakash & Upendra Nath Dwivedi
Pages: 660-672
Published online: 11 Mar 2019
AbstractforIdentification of repurposed protein kinase B binders from FDA-approved drug library: a hybrid–structure activity relationship and systems modeling based approach | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 251 Views
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Article
Symmetrization of the backbone of nucleic acids: a molecular dynamics study
Pradeep Pant, Amita Pathak & B. Jayaram
Pages: 673-681
Published online: 26 Mar 2019
AbstractforSymmetrization of the backbone of nucleic acids: a molecular dynamics study | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 311 Views
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Article
Identification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches
Rajendran Selvakumar, Dhanabalan Anantha Krishnan, Chandrasekaran Ramakrishnan, Devadasan Velmurugan & Krishnasamy Gunasekaran
Pages: 682-696
Published online: 22 Mar 2019
AbstractforIdentification of novel NAD(P)H dehydrogenase [quinone] 1 antagonist using computational approaches | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 221 Views
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Article
Carbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach
Zohre Hasanzade & Heidar Raissi
Pages: 697-707
Published online: 22 Mar 2019
AbstractforCarbon and boron nanotubes as a template material for adsorption of 6-Thioguanine chemotherapeutic: a molecular dynamics and density functional approach | Full Text | References | PDF (2 MB) | EPUB
  • 209 Views
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Article
Impact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations
Suniba Shuaib, Rajneet Kaur Saini, Deepti Goyal & Bhupesh Goyal
Pages: 708-721
Published online: 02 Apr 2019
AbstractforImpact of K16A and K28A mutation on the structure and dynamics of amyloid-β42 peptide in Alzheimer’s disease: key insights from molecular dynamics simulations | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 405 Views
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Article
Characterization of interactions between cromolyn sodium and bovine serum albumin by spectroscopic, calorimetric and computational methods
Shama Yasmeen, Riyazuddeen, Samima Khatun & Faizan Abul Qais
Pages: 722-732
Published online: 26 Mar 2019
AbstractforCharacterization of interactions between cromolyn sodium and bovine serum albumin by spectroscopic, calorimetric and computational methods | Full Text | References | PDF (1.7 MB) | EPUB
  • 193 Views
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Article
Syntheses, characterization, DNA/HSA binding ability and antitumor activities of a family of isostructural binuclear lanthanide complexes containing hydrazine Schiff base
Xue-Qing Song, Zhi-Gang Wang, Yang Wang, Yu-Ying Huang, Yu-Xuan Sun, Yan Ouyang, Cheng-Zhi Xie & Jing-Yuan Xu
Pages: 733-743
Published online: 26 Mar 2019
AbstractforSyntheses, characterization, DNA/HSA binding ability and antitumor activities of a family of isostructural binuclear lanthanide complexes containing hydrazine Schiff base | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 326 Views
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Article
Assessment on the binding affinity between ritonavir with model transport protein: a combined multi-spectroscopic approaches with computer simulation
Bao-Li Wang, Kai-Li Zhou, Yan-Yue Lou, Dong-Qi Pan, Song-Bo Kou, Zhen-Yi Lin & Jie-Hua Shi
Pages: 744-755
Published online: 11 Mar 2019
AbstractforAssessment on the binding affinity between ritonavir with model transport protein: a combined multi-spectroscopic approaches with computer simulation | Full Text | References | PDF (2.7 MB) | EPUB
  • 157 Views
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Article
Synthesis, FT-IR and NMR characterization, antimicrobial activity, cytotoxicity and DNA docking analysis of a new anthraquinone derivate compound
Sefa Celik, Funda Ozkok, Aysen E. Ozel, Yesim Müge Sahin, Sevim Akyuz, Belgi Diren Sigirci, Beren Basaran Kahraman, Hakan Darici & Erdal Karaoz
Pages: 756-770
Published online: 02 Apr 2019
AbstractforSynthesis, FT-IR and NMR characterization, antimicrobial activity, cytotoxicity and DNA docking analysis of a new anthraquinone derivate compound | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 872 Views
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Article
Structural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer
Ramireddy Sriroopreddy, P. Raghuraman & C. Sudandiradoss
Pages: 771-780
Published online: 19 Mar 2019
AbstractforStructural debilitation of mutation G322D associated with MSH2 and their role in triple negative breast cancer | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 133 Views
  • 3 CrossRef citations
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Article
Spectral analysis of molecular dynamics simulations on PDZ: MD sectors
Bharat Lakhani, Kelly M. Thayer, Emily Black & David L. Beveridge
Pages: 781-790
Published online: 01 Jul 2019
AbstractforSpectral analysis of molecular dynamics simulations on PDZ: MD sectors | Full Text | References | PDF (2 MB) | EPUB
  • 1980 Views
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Open Access
Article
Identification of new DNA gyrase inhibitors based on bioactive compounds from streptomyces: structure-based virtual screening and molecular dynamics simulations approaches
Hourieh Kalhor, Solmaz Sadeghi, Mahya Marashiyan, Reyhaneh Kalhor, Sanaz Aghaei Gharehbolagh, Mohammad Reza Akbari Eidgahi & Hamzeh Rahimi
Pages: 791-806
Published online: 27 Mar 2019
AbstractforIdentification of new DNA gyrase inhibitors based on bioactive compounds from streptomyces: structure-based virtual screening and molecular dynamics simulations approaches | Full Text | References | PDF (3 MB) | EPUB
  • 342 Views
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Article
Understanding ligands driven mechanism of wild and mutant aryl hydrocarbon receptor in presence of phytochemicals combating Parkinson’s disease: an in silico and in vivo study
Surya Narayan Rath, Lingaraja Jena & Manorama Patri
Pages: 807-826
Published online: 02 Apr 2019
AbstractforUnderstanding ligands driven mechanism of wild and mutant aryl hydrocarbon receptor in presence of phytochemicals combating Parkinson’s disease: an in silico and in vivo study | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 442 Views
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Article
Molecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428
Aditi Singh, Mriganko Das & Abhinav Grover
Pages: 827-840
Published online: 19 Mar 2019
AbstractforMolecular mechanism of acetoacetyl-CoA enhanced kinetics for increased bioplastic production from Cupriavidus necator 428 | Full Text | References | PDF (7.4 MB) | EPUB | Supplemental
  • 420 Views
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Article
Synthesis, anticholinesterase activity and molecular modeling studies of novel carvacrol-substituted amide derivatives
Belma Zengin Kurt, Serdar Durdagi, Gulsen Celebi, Ramin Ekhteiari Salmas & Fatih Sonmez
Pages: 841-859
Published online: 20 Apr 2019
AbstractforSynthesis, anticholinesterase activity and molecular modeling studies of novel carvacrol-substituted amide derivatives | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 462 Views
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Article
Design of novel dopamine D2 and serotonin 5-HT2A receptors dual antagonists toward schizophrenia: An integrated study with QSAR, molecular docking, virtual screening and molecular dynamics simulations
Cuihua Zhang, Qunlin Li, Lingwei Meng & Yujie Ren
Pages: 860-885
Published online: 27 Mar 2019
AbstractforDesign of novel dopamine D2 and serotonin 5-HT2A receptors dual antagonists toward schizophrenia: An integrated study with QSAR, molecular docking, virtual screening and molecular dynamics simulations | Full Text | References | PDF (9 MB) | EPUB
  • 658 Views
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Article
Identification of human tau-tubulin kinase 1 inhibitors: an integrated e-pharmacophore-based virtual screening and molecular dynamics simulation
Srabanti Jana & Sushil Kumar Singh
Pages: 886-900
Published online: 02 Apr 2019
AbstractforIdentification of human tau-tubulin kinase 1 inhibitors: an integrated e-pharmacophore-based virtual screening and molecular dynamics simulation | Full Text | References | PDF (6.1 MB) | EPUB | Supplemental
  • 329 Views
  • 9 CrossRef citations
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Article
Halogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy
Nizam Uddin, Sinthyia Ahmed, Akib Mahmud Khan, Mohammad Mazharol Hoque & Mohammad A. Halim
Pages: 901-917
Published online: 02 Apr 2019
AbstractforHalogenated derivatives of methotrexate as human dihydrofolate reductase inhibitors in cancer chemotherapy | Full Text | References | PDF (3.5 MB) | EPUB
  • 387 Views
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Letters to the Editor

Letter
Nitroxidized-HSA induced oxidative damage in human erythrocytes: an ex vivo approach
Akhlas Tarannum, Zarina Arif, Khursheed Alam & Moinuddin
Pages: 918-927
Published online: 19 Mar 2019
First Page PreviewforNitroxidized-HSA induced oxidative damage in human erythrocytes: an ex vivo approach | Full Text | References | PDF (2.6 MB) | EPUB
  • 57 Views
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Letter
An oxidodiperoxido vanadium-based artificial nuclease: DNA binding and cleavage studies
Haimanti Adhikari, Rina Ghosh & Kalyan K. Mukherjea
Pages: 928-933
Published online: 02 Apr 2019
AbstractforAn oxidodiperoxido vanadium-based artificial nuclease: DNA binding and cleavage studies | Full Text | References | PDF (1.5 MB) | EPUB
  • 79 Views
  • 2 CrossRef citations
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Letter
Multispectral and molecular docking investigations on the interaction of primethamine/trimethoprim with BSA/HSA
Xiaoyue Sun, Shuyun Bi, Jun Wu, Rui Zhao, Di Shao & Zhe Song
Pages: 934-942
Published online: 19 Mar 2019
AbstractforMultispectral and molecular docking investigations on the interaction of primethamine/trimethoprim with BSA/HSA | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 364 Views
  • 20 CrossRef citations
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Letter
Interaction of aspartic acid and asparagine with RNA nucleobases: a quantum chemical view
Deepika Kagra, S. P. Preethi & Purshotam Sharma
Pages: 943-955
Published online: 02 Apr 2019
AbstractforInteraction of aspartic acid and asparagine with RNA nucleobases: a quantum chemical view | Full Text | References | PDF (3.9 MB) | EPUB
  • 245 Views
  • 6 CrossRef citations
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