Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 9 (2019)

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Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 9 (2019)

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Research Article

Article
Exploring potentially alternative non-canonical DNA duplex structures through simulation
Rodrigo Galindo-Murillo, Thomas E. Cheatham III & Robert C. Hopkins
Pages: 2201-2210
Published online: 17 Nov 2018
AbstractforExploring potentially alternative non-canonical DNA duplex structures through simulation | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 234 Views
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Article
Metal sensitive and DNA concentration dependent structural rearrangement of short oligonucleotide into large suprastructures
J. Shankaraswamy, Shikhar Tyagi, Anju Singh, Daisuke Miyoshi & Sarika Saxena
Pages: 2211-2218
Published online: 28 Dec 2018
AbstractforMetal sensitive and DNA concentration dependent structural rearrangement of short oligonucleotide into large suprastructures | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 176 Views
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Article
Insights into the DNA binding induced thermal stabilization of transcription factor FOXP3
Amresh Prakash, Vijay Kumar, Andrew M. Lynn & Rizwanul Haque
Pages: 2219-2229
Published online: 13 Nov 2018
AbstractforInsights into the DNA binding induced thermal stabilization of transcription factor FOXP3 | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 198 Views
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Article
Deciphering the binding of carbendazim (fungicide) with human serum albumin: A multi-spectroscopic and molecular modelling studies
Mohd Faizan Siddiqui, Mohd Shahnawaz Khan, Fohad Mabood Husain & Bilqees Bano
Pages: 2230-2241
Published online: 17 Nov 2018
AbstractforDeciphering the binding of carbendazim (fungicide) with human serum albumin: A multi-spectroscopic and molecular modelling studies | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 294 Views
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Article
In vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods
Neda Hosseinpour Moghadam, Sadegh Salehzadeh, Hamid Tanzadehpanah, Massoud Saidijam, Jamshid Karimi & Sadegh Khazalpour
Pages: 2242-2253
Published online: 13 Nov 2018
AbstractforIn vitro cytotoxicity and DNA/HSA interaction study of triamterene using molecular modelling and multi-spectroscopic methods | Full Text | References | PDF (3.2 MB) | EPUB
  • 285 Views
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Article
Human serum albumin–malathion complex study in the presence of silver nanoparticles at different sizes by multi spectroscopic techniques
Parisa Teimoori Baghaee, Adeleh Divsalar, Jamshikhan Chamani & Atena Donya
Pages: 2254-2264
Published online: 23 Dec 2018
AbstractforHuman serum albumin–malathion complex study in the presence of silver nanoparticles at different sizes by multi spectroscopic techniques | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 240 Views
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Article
Isothermal titration calorimetry and stopped flow circular dichroism investigations of the interaction between lomefloxacin and human serum albumin in the presence of amino acids
Sima Beigoli, Atena Sharifi Rad, Azam Askari, Reza Assaran Darban & Jamshidkhan Chamani
Pages: 2265-2282
Published online: 26 Nov 2018
AbstractforIsothermal titration calorimetry and stopped flow circular dichroism investigations of the interaction between lomefloxacin and human serum albumin in the presence of amino acids | Full Text | References | PDF (4.1 MB) | EPUB
  • 492 Views
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Article
Electronic and fluorescent studies on the interaction of DNA and BSA with a new ternary praseodymium complex containing 2,9-dimethyl 1,10-phenanthroline and antibacterial activities testing
Zohreh Moradi, Mozhgan Khorasani-Motlagh, Ali Reza Rezvani & Meissam Noroozifar
Pages: 2283-2295
Published online: 01 Nov 2018
AbstractforElectronic and fluorescent studies on the interaction of DNA and BSA with a new ternary praseodymium complex containing 2,9-dimethyl 1,10-phenanthroline and antibacterial activities testing | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 221 Views
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Article
Deciphering the binding mode and mechanistic insights of pentadecylidenemalonate (1b) as activator of histone acetyltransferase PCAF
Venkatesan Suryanarayanan & Sanjeev Kumar Singh
Pages: 2296-2309
Published online: 04 Nov 2018
AbstractforDeciphering the binding mode and mechanistic insights of pentadecylidenemalonate (1b) as activator of histone acetyltransferase PCAF | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 154 Views
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Article
Structure-based prediction of West Nile virus-human protein–protein interactions
Jing Chen, Jun Sun, Xiangming Liu, Feng Liu, Rong Liu & Jia Wang
Pages: 2310-2321
Published online: 17 Nov 2018
AbstractforStructure-based prediction of West Nile virus-human protein–protein interactions | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 305 Views
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Article
Genome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences
V.R. Chechetkin & V.V. Lobzin
Pages: 2322-2338
Published online: 22 Nov 2018
AbstractforGenome packaging within icosahedral capsids and large-scale segmentation in viral genomic sequences | Full Text | References | PDF (2.4 MB) | EPUB
  • 196 Views
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Article
Investigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis
Kandasamy Saravanan, Magudeeswaran Sivanandam, Govindasamy Hunday, Lakshmanan Mathiyalagan & Poomani Kumaradhas
Pages: 2339-2354
Published online: 19 Nov 2018
AbstractforInvestigation of intermolecular interactions and stability of verubecestat in the active site of BACE1: Development of first model from QM/MM-based charge density and MD analysis | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 405 Views
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Article
Extrapolation of phenolic compounds as multi-target agents against cancer and inflammation
Naresh Kumar, Saurabh Gupta, Tara Chand Yadav, Vikas Pruthi, Pritish Kumar Varadwaj & Nidhi Goel
Pages: 2355-2369
Published online: 10 Dec 2018
AbstractforExtrapolation of phenolic compounds as multi-target agents against cancer and inflammation | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 444 Views
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Article
Antimicrobial cell penetrating peptides with bacterial cell specificity: pharmacophore modelling, quantitative structure activity relationship and molecular dynamics simulation
Mbuso Faya, Rahul S. Kalhapure, Dinesh Dhumal, Nikhil Agrawal, Calvin Omolo, Krishnacharya G. Akamanchi & Thirumala Govender
Pages: 2370-2380
Published online: 13 Nov 2018
AbstractforAntimicrobial cell penetrating peptides with bacterial cell specificity: pharmacophore modelling, quantitative structure activity relationship and molecular dynamics simulation | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 574 Views
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Article
Exploratory algorithm to devise multi-epitope subunit vaccine by investigating Leishmania donovani membrane proteins
Nazia Khatoon, Rajan Kumar Pandey, Rupal Ojha, Veeranarayanan Surya Aathmanathan, Muthukalingan Krishnan & Vijay Kumar Prajapati
Pages: 2381-2393
Published online: 10 Dec 2018
AbstractforExploratory algorithm to devise multi-epitope subunit vaccine by investigating Leishmania donovani membrane proteins | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 222 Views
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Article
Exploring a potential allosteric inhibition mechanism in the motor domain of human Eg-5
Shanthi Nagarajan & Sugunadevi Sakkiah
Pages: 2394-2403
Published online: 13 Nov 2018
AbstractforExploring a potential allosteric inhibition mechanism in the motor domain of human Eg-5 | Full Text | References | PDF (2.7 MB) | EPUB
  • 165 Views
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Article
Molecular dynamics insights for PI3K-δ inhibition & structure guided identification of novel PI3K-δ inhibitors
Shubham Srivastava, Bhanwar Singh Choudhary, Pakhuri Mehta, Sukanya, Manish Sharma & Ruchi Malik
Pages: 2404-2414
Published online: 18 Nov 2018
AbstractforMolecular dynamics insights for PI3K-δ inhibition & structure guided identification of novel PI3K-δ inhibitors | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 320 Views
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Article
Exploring binding modes of the selected inhibitors to phosphodiesterase delta by all-atom molecular dynamics simulations and free energy calculations
Hui Zhong, Yan-Jun Zhang & Xiao-Bin Shan
Pages: 2415-2429
Published online: 10 Jan 2019
AbstractforExploring binding modes of the selected inhibitors to phosphodiesterase delta by all-atom molecular dynamics simulations and free energy calculations | Full Text | References | PDF (2.8 MB) | EPUB
  • 133 Views
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Article
Identification of protegrin-1 as a stable and nontoxic scaffold among protegrin family – a computational approach
S. R. Shruti & R. Rajasekaran
Pages: 2430-2439
Published online: 05 Dec 2018
AbstractforIdentification of protegrin-1 as a stable and nontoxic scaffold among protegrin family – a computational approach | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 119 Views
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Article
Probing the “fingers” domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations
Saravanan Manjula, Magudeeswaran Sivanandam & Poomani Kumaradhas
Pages: 2440-2456
Published online: 13 Nov 2018
AbstractforProbing the “fingers” domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking, molecular dynamics simulation and binding free energy calculations | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 259 Views
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Article
Determination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation
Burcu Bayel Secinti, Gizem Tatar & Tugba Taskin Tok
Pages: 2457-2463
Published online: 26 Oct 2018
AbstractforDetermination of potential selective inhibitors for ROCKI and ROCKII isoforms with molecular modeling techniques: structure based docking, ADMET and molecular dynamics simulation | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 407 Views
  • 15 CrossRef citations
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Article
Novel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models
Mehreen Zaka, Bilal Haider Abbasi & Serdar Durdagi
Pages: 2464-2476
Published online: 23 Dec 2018
AbstractforNovel tumor necrosis factor-α (TNF-α) inhibitors from small molecule library screening for their therapeutic activity profiles against rheumatoid arthritis using target-driven approaches and binary QSAR models | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 677 Views
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