Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 6 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 6 (2021)

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Research Articles

Article
Hybridization kinetics of DNA fragments in the presence of ligands intercalating into DNA-duplexes
Valeri B. Arakelyan, Aleksandr Y. Mamasakhlisov, Eduard M. Kazaryan, Marine A. Parsadanyan & Poghos O. Vardevanyan
Pages: 1907-1911
Published online: 16 Mar 2020
AbstractforHybridization kinetics of DNA fragments in the presence of ligands intercalating into DNA-duplexes | Full Text | References | PDF (810.5 KB) | EPUB
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Article
In silico studies of the inhibition mechanism of dengue with papain
Vasudevan Saranya, Ramachandran Radhika, Ramasamy Shankar & Subramaniam Vijayakumar
Pages: 1912-1927
Published online: 06 Apr 2020
AbstractforIn silico studies of the inhibition mechanism of dengue with papain | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 236 Views
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Article
Identification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation
Guoyi Yan, Dongxiao Li, Xinxin Zhong, Ge Liu, Xueqin Wang, Yuanxiang Lu, Fangyuan Qin, Yuqi Guo, Shaofeng Duan & Deyu Li
Pages: 1928-1939
Published online: 11 Apr 2020
AbstractforIdentification of HDAC6 selective inhibitors: pharmacophore based virtual screening, molecular docking and molecular dynamics simulation | Full Text | References | PDF (3.6 MB) | EPUB
  • 566 Views
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Article
Deciphering the impact of missense mutations on structure and dynamics of SMAD4 protein involved in pathogenesis of gall bladder cancer
Rakesh Kumar, Rahul Kumar, Pranay Tanwar, G. K. Rath, Ritesh Kumar, Sunil Kumar, Nihar Dash, Prasenjit Das & Showket Hussain
Pages: 1940-1954
Published online: 17 Mar 2020
AbstractforDeciphering the impact of missense mutations on structure and dynamics of SMAD4 protein involved in pathogenesis of gall bladder cancer | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 231 Views
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Article
The role of benzylic-allylic hydrogen atoms on the antiradical activity of prenylated natural chalcones: a thermodynamic and kinetic study
Houssem Boulebd
Pages: 1955-1964
Published online: 20 Mar 2020
AbstractforThe role of benzylic-allylic hydrogen atoms on the antiradical activity of prenylated natural chalcones: a thermodynamic and kinetic study | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 179 Views
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Article
Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation
Khattab Al-Khafaji & Tugba Taskin Tok
Pages: 1965-1974
Published online: 24 Mar 2020
AbstractforAmygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 413 Views
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Article
Potential target identification for breast cancer and screening of small molecule inhibitors: A bioinformatics approach
Shivangi Agarwal & Sushil K. Kashaw
Pages: 1975-1989
Published online: 25 Mar 2020
AbstractforPotential target identification for breast cancer and screening of small molecule inhibitors: A bioinformatics approach | Full Text | References | PDF (4.5 MB) | EPUB | Supplemental
  • 352 Views
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Article
Exploring the interaction of Peloruside-A with drug resistant αβII and αβIII tubulin isotypes in human ovarian carcinoma using a molecular modeling approach
Bajarang Vasant Kumbhar & Vishwambhar Vishnu Bhandare
Pages: 1990-2002
Published online: 03 Apr 2020
AbstractforExploring the interaction of Peloruside-A with drug resistant αβII and αβIII tubulin isotypes in human ovarian carcinoma using a molecular modeling approach | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 239 Views
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Article
Molecular dynamics simulations of copper binding to N-terminus mutants of amyloid-β
Oliver D. Kennedy-Britten, Nadiyah Al-Shammari & James A. Platts
Pages: 2003-2013
Published online: 02 Apr 2020
AbstractforMolecular dynamics simulations of copper binding to N-terminus mutants of amyloid-β | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 303 Views
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Article
Bioconjugation of gold nanoparticles with aminoguanidine as a potential inhibitor of non-enzymatic glycation reaction
Yixuan Wang, Hongyong Wang, Mohd. Shahnawaz Khan, Fohad Mabood Husain, Saheem Ahmad & Li Bian
Pages: 2014-2020
Published online: 09 Apr 2020
AbstractforBioconjugation of gold nanoparticles with aminoguanidine as a potential inhibitor of non-enzymatic glycation reaction | Full Text | References | PDF (1 MB) | EPUB
  • 199 Views
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Article
Pharmacophore- based virtual screening, 3D- QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors
Bhumi M. Shah, Palmi Modi & Priti Trivedi
Pages: 2021-2043
Published online: 07 May 2020
AbstractforPharmacophore- based virtual screening, 3D- QSAR, molecular docking approach for identification of potential dipeptidyl peptidase IV inhibitors | Full Text | References | PDF (5.2 MB) | EPUB | Supplemental
  • 392 Views
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Article
Unraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana
Clauber Henrique Souza da Costa, Ted Wilson Bichara, Guelber Cardoso Gomes, Alberto Monteiro dos Santos, Kauê Santana da Costa, Anderson Henrique Lima e Lima, Cláudio Nahum Alves & Jerônimo Lameira
Pages: 2044-2055
Published online: 25 Mar 2020
AbstractforUnraveling the conformational dynamics of glycerol 3-phosphate dehydrogenase, a nicotinamide adenine dinucleotide-dependent enzyme of Leishmania mexicana | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 305 Views
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Article
In silico screening of FDA approved drugs on AXL kinase and validation for breast cancer cell line
Lavanya Nagamalla & J. V. Shanmukha Kumar
Pages: 2056-2070
Published online: 26 Mar 2020
AbstractforIn silico screening of FDA approved drugs on AXL kinase and validation for breast cancer cell line | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 311 Views
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Article
Comparative modeling and structure based drug repurposing of PAX2 transcription factor for targeting acquired chemoresistance in pancreatic ductal adenocarcinoma
Imlimaong Aier, Rahul Semwal, Utkarsh Raj & Pritish Kumar Varadwaj
Pages: 2071-2078
Published online: 25 Mar 2020
AbstractforComparative modeling and structure based drug repurposing of PAX2 transcription factor for targeting acquired chemoresistance in pancreatic ductal adenocarcinoma | Full Text | References | PDF (1.7 MB) | EPUB
  • 183 Views
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Article
Molecular docking and molecular dynamics simulations of a mutant Acinetobacter haemolyticus alkaline-stable lipase against tributyrin
Nurul Fatin Syamimi Khairul Anuar, Roswanira Abdul Wahab, Fahrul Huyop, Syazwani Itri Amran, Azzmer Azzar Abdul Hamid, Khairul Bariyyah Abd Halim & Mohammad Hakim Mohammad Hood
Pages: 2079-2091
Published online: 23 Mar 2020
AbstractforMolecular docking and molecular dynamics simulations of a mutant Acinetobacter haemolyticus alkaline-stable lipase against tributyrin | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 442 Views
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Article
Molecular docking, DFT and antimicrobial studies of Cu(II) complex as topoisomerase I inhibitor
Shazia Parveen, Farukh Arjmand, Qianfan Zhang, Musheer Ahmad, Arif Khan & Loic Toupet
Pages: 2092-2105
Published online: 25 Mar 2020
AbstractforMolecular docking, DFT and antimicrobial studies of Cu(II) complex as topoisomerase I inhibitor | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 314 Views
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Article
Global transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses in Oryza sativa (L.)
Pandiyan Muthuramalingam, Rajendran Jeyasri, Anthonymuthu Selvaraj, Dhamodharan Kalaiyarasi, Wilson Aruni, Shunmugiah Thevar Karutha Pandian & Manikandan Ramesh
Pages: 2106-2117
Published online: 10 Apr 2020
AbstractforGlobal transcriptome analysis of novel stress associated protein (SAP) genes expression dynamism of combined abiotic stresses in Oryza sativa (L.) | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 372 Views
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Article
In silico strategies for probing novel DPP-IV inhibitors as anti-diabetic agents
Shweta Sharma, Shubham Srivastav, Garima Singh, Smrita Singh, Ruchi Malik, Mohammad Mumtaz Alam, Mohammad Shaqiquzamman, Shakir Ali & Mymoona Akhter
Pages: 2118-2132
Published online: 20 Apr 2020
AbstractforIn silico strategies for probing novel DPP-IV inhibitors as anti-diabetic agents | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 219 Views
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Article
Functional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches
Shang-Jun Yin, Min-Woo Park, Bit-Na Lee, Jun-Mo Yang, Yong-Doo Park & Guo-Ying Qian
Pages: 2133-2151
Published online: 07 Apr 2020
AbstractforFunctional study of acetaldehyde dehydrogenase 1 (ALDH1) in keratinocytes: microarray integrating bioinformatics approaches | Full Text | References | PDF (5.2 MB) | EPUB | Supplemental
  • 282 Views
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Article
Cloning, expression, homology modelling and molecular dynamics simulation of four domain-containing α-amylase from Streptomyces griseus
Selvaraj Alagu Lakshmi, RajaMohamed Beema Shafreen, Kannan Balaji, Kalibulla Syed Ibrahim, Sugathan Shiburaj, Valsala Gayathri & Shunmugiah Karutha Pandian
Pages: 2152-2163
Published online: 26 Mar 2020
AbstractforCloning, expression, homology modelling and molecular dynamics simulation of four domain-containing α-amylase from Streptomyces griseus | Full Text | References | PDF (3.1 MB) | EPUB
  • 277 Views
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Article
Antimicrobial activity of ginger on cariogenic bacteria: molecular networking and molecular docking analyses
Laleh Babaeekhou & Maryam Ghane
Pages: 2164-2175
Published online: 28 Mar 2020
AbstractforAntimicrobial activity of ginger on cariogenic bacteria: molecular networking and molecular docking analyses | Full Text | References | PDF (2 MB) | EPUB
  • 645 Views
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Article
Synthesis, evaluation, molecular dynamics simulation and targets identification of novel pyrazole-containing imide derivatives
Wenxi Cai, Jingwei Wu, Yingzhan Sun, Ailin Liu, Runling Wang, Ying Ma, Shuqing Wang & Weili Dong
Pages: 2176-2188
Published online: 31 Mar 2020
AbstractforSynthesis, evaluation, molecular dynamics simulation and targets identification of novel pyrazole-containing imide derivatives | Full Text | References | PDF (2.4 MB) | EPUB
  • 294 Views
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Article
In silico design of peptide inhibitors of tubulin: amyloid-β as a lead compound
Nima Razzaghi-Asl & Ahmad Ebadi
Pages: 2189-2198
Published online: 28 Mar 2020
AbstractforIn silico design of peptide inhibitors of tubulin: amyloid-β as a lead compound | Full Text | References | PDF (2.2 MB) | EPUB
  • 187 Views
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Article
Molecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites
Romualdo Troisi, Nicole Balasco, Luigi Vitagliano & Filomena Sica
Pages: 2199-2209
Published online: 07 Apr 2020
AbstractforMolecular dynamics simulations of human α-thrombin in different structural contexts: evidence for an aptamer-guided cooperation between the two exosites | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 362 Views
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Article
An in-silico approach: identification of PPAR-γ agonists from seaweeds for the management of Alzheimer’s Disease
Satvik Kotha, Swapna B.Vithal M. Kulkarni, Ramachandra Setty S.Harish Kumar B.Harisha R.
Pages: 2210-2229
Published online: 15 Apr 2020
AbstractforAn in-silico approach: identification of PPAR-γ agonists from seaweeds for the management of Alzheimer’s Disease | Full Text | References | PDF (6.1 MB) | EPUB
  • 406 Views
  • 10 CrossRef citations
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Article
A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube
Farzane Abasi Joozdani & Majid Taghdir
Pages: 2230-2241
Published online: 15 Apr 2020
AbstractforA molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 181 Views
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Article
DNA binding, antibacterial, hemolytic and anticancer studies of some fluorescent emissive surfactant-ruthenium(II) complexes
Selvan Nehru, Selvakumar Veeralakshmi, Siva Kalaiselvam, S.P. Subin David, Jayakumar Sandhya & Sankaralingam Arunachalam
Pages: 2242-2256
Published online: 15 Apr 2020
AbstractforDNA binding, antibacterial, hemolytic and anticancer studies of some fluorescent emissive surfactant-ruthenium(II) complexes | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 363 Views
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Article
Synthesis of niobium substituted cobalt-nickel nano-ferrite (Co0.5Ni0.5NbxFe2-xO4 (x ≤ 0.1) by hydrothermal approach show strong anti-colon cancer activities
H. Tombuloglu, F.A. Khan, M.A. Almessiere, S. Aldakheel & A. Baykal
Pages: 2257-2265
Published online: 07 Apr 2020
AbstractforSynthesis of niobium substituted cobalt-nickel nano-ferrite (Co0.5Ni0.5NbxFe2-xO4 (x ≤ 0.1) by hydrothermal approach show strong anti-colon cancer activities | Full Text | References | PDF (2.9 MB) | EPUB
  • 349 Views
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Article
Distribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules
Víctor Martínez, Christian Schaerer, Pablo Hernández, Dora B. Krimer, Jorge B. Schvartzman & María-José Fernández-Nestosa
Pages: 2266-2277
Published online: 10 Apr 2020
AbstractforDistribution of torsional stress between the un-replicated and replicated regions in partially replicated molecules | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 159 Views
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Letters to the Editor

Letter
Binding efficacy of aminobenzoic acid derivatives with DNA duplex: drug binding sites and DNA structure and dynamics
P. Chanphai, F. Cloutier, C. Reyes-Moreno, G. Bérubé & H. A. Tajmir-Riahi
Pages: 2278-2283
Published online: 24 Mar 2020
AbstractforBinding efficacy of aminobenzoic acid derivatives with DNA duplex: drug binding sites and DNA structure and dynamics | Full Text | References | PDF (1.5 MB) | EPUB
  • 96 Views
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Letter
Effect of monovalent ions on the thermal stability of bovine serum albumin in dimethylsulfoxide aqueous solutions. Spectroscopic approach
Karine Grigoryan, Ashkhen Zatikyan & Hasmik Shilajyan
Pages: 2284-2288
Published online: 31 Mar 2020
First Page PreviewforEffect of monovalent ions on the thermal stability of bovine serum albumin in dimethylsulfoxide aqueous solutions. Spectroscopic approach | Full Text | References | PDF (740.4 KB) | EPUB
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