Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 16 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 16 (2020)

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Research Articles

Article
Novel inhibitors of Rho-kinase mediated neuroinflammatory pathways and their potential application in recovery of injured spinal cord
Mallikarjuna Nimgampalle, Hemanth Naick Banavath, Harshini Chakravarthy, Ambrish Saxena & Vasudharani Devanathan
Pages: 4669-4686
Published online: 15 Nov 2019
AbstractforNovel inhibitors of Rho-kinase mediated neuroinflammatory pathways and their potential application in recovery of injured spinal cord | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 242 Views
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Article
Potential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations
Ryan S. Ramos, Williams J. C. Macêdo, Josivan S. Costa, Carlos H. T. de P. da Silva, Joaquín M. C. Rosa, Jorddy Neves da Cruz, Mozaniel S. de Oliveira, Eloisa H. de Aguiar Andrade, Raullyan B. L. e Silva, Raimundo N. P. Souto & Cleydson B. R. Santos
Pages: 4687-4709
Published online: 11 Nov 2019
AbstractforPotential inhibitors of the enzyme acetylcholinesterase and juvenile hormone with insecticidal activity: study of the binding mode via docking and molecular dynamics simulations | Full Text | References | PDF (4.4 MB) | EPUB
  • 1000 Views
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Article
Targeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction
Shabnam Mahernia, Malihe Hassanzadeh, Sajad Sarvari & Massoud Amanlou
Pages: 4710-4717
Published online: 03 Dec 2019
AbstractforTargeting the microRNA binding domain of argonaute 2: rational inhibitor design and study of mutation effects on protein-ligand interaction | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 291 Views
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Article
The mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations
Gábor Balogh, István Komáromi & Zsuzsanna Bereczky
Pages: 4718-4732
Published online: 12 Nov 2019
AbstractforThe mechanism of high affinity pentasaccharide binding to antithrombin, insights from Gaussian accelerated molecular dynamics simulations | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 1642 Views
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Open Access
Article
Refined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents
Zhenhai Pan, Ying Wang, Xi Gu, Jian Wang & Maosheng Cheng
Pages: 4733-4745
Published online: 06 Nov 2019
AbstractforRefined homology model of cytochrome bcc complex B subunit for virtual screening of potential anti-tuberculosis agents | Full Text | References | PDF (4.6 MB) | EPUB
  • 281 Views
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Article
Experimental and theoretical investigations of Dy(III) complex with 2,2′-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study
Zahra Aramesh-Boroujeni, Shohreh Jahani, Mozhgan Khorasani-Motlagh, Kagan Kerman, Nahal Aramesh, Saeid Asadpour & Meissam Noroozifar
Pages: 4746-4763
Published online: 14 Nov 2019
AbstractforExperimental and theoretical investigations of Dy(III) complex with 2,2′-bipyridine ligand: DNA and BSA interactions and antimicrobial activity study | Full Text | References | PDF (4.5 MB) | EPUB
  • 189 Views
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Article
Nucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants
Wei Dan, Yan Jin, Zizhong Tang, Yongmin Li & Huipeng Yao
Pages: 4764-4773
Published online: 13 Nov 2019
AbstractforNucleotide composition and synonymous codon usage of open reading frames in Norovirus GII.4 variants | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 227 Views
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Article
A new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances
Ol’ha O. Brovarets’ & Dmytro M. Hovorun
Pages: 4774-4800
Published online: 16 Dec 2019
AbstractforA new era of the prototropic tautomerism of the quercetin molecule: A QM/QTAIM computational advances | Full Text | References | PDF (7.5 MB) | EPUB
  • 125 Views
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Article
Cationic porphyrins as destabilizer of a G-quadruplex located at the promoter of human MYH7 β gene
Anju Singh, Savita Joshi & Shrikant Kukreti
Pages: 4801-4816
Published online: 06 Dec 2019
AbstractforCationic porphyrins as destabilizer of a G-quadruplex located at the promoter of human MYH7 β gene | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 323 Views
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Article
Molecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation
Rabeeh Khorrampour & Heidar Raissi
Pages: 4817-4826
Published online: 20 Nov 2019
AbstractforMolecular insight into adsorption affinities of Carmustine drug on boron and nitrogen doped functionalized single-walled carbon nanotubes using density functional theory including dispersion correction calculations and molecular dynamics simulation | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 178 Views
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Article
Targeting the NTPase site of Zika virus NS3 helicase for inhibitor discovery
Deepak Kumar, Murali Aarthy, Prateek Kumar, Sanjeev Kumar Singh, Vladimir N. Uversky & Rajanish Giri
Pages: 4827-4837
Published online: 14 Nov 2019
AbstractforTargeting the NTPase site of Zika virus NS3 helicase for inhibitor discovery | Full Text | References | PDF (3.4 MB) | EPUB
  • 546 Views
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Article
Evaluation of some genes and proteins involved in apoptosis on human chronic myeloid leukemia cells (K562 cells) by datura innoxia leaves aqueous extract
Elham Chamani, Zohreh Rezaei, Kazem Dastjerdi, Setareh Javanshir, Khatereh Khorsandi & Gholam Abbas Mohammadi
Pages: 4838-4849
Published online: 27 Nov 2019
AbstractforEvaluation of some genes and proteins involved in apoptosis on human chronic myeloid leukemia cells (K562 cells) by datura innoxia leaves aqueous extract | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 154 Views
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Article
Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches
Zulkar Nain, Faruq Abdulla, M. Mizanur Rahman, Mohammad Minnatul Karim, Md. Shakil Ahmed Khan, Sifat Bin Sayed, Shafi Mahmud, S. M. Raihan Rahman, Md. Moinuddin Sheam, Zahurul Haque & Utpal Kumar Adhikari
Pages: 4850-4867
Published online: 20 Nov 2019
AbstractforProteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches | Full Text | References | PDF (4.9 MB) | EPUB | Supplemental
  • 628 Views
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Article
Molecular dynamics complemented by site-directed mutagenesis reveals significant difference between the interdomain salt bridge networks stabilizing oligopeptidases B from bacteria and protozoa in their active conformations
Dmitry E. Petrenko, Anna G. Mikhailova, Vladimir I. Timofeev, Yulia К. Agapova, David M. Karlinsky, Aleksandr S. Komolov, Dmitry A. Korzhenevskiy, Anna V. Vlaskina, Lev D. Rumsh & Tatiana V. Rakitina
Pages: 4868-4882
Published online: 25 Nov 2019
AbstractforMolecular dynamics complemented by site-directed mutagenesis reveals significant difference between the interdomain salt bridge networks stabilizing oligopeptidases B from bacteria and protozoa in their active conformations | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 137 Views
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Review Article

Review Article
Electrostatic interactions in molecular recognition of intrinsically disordered proteins
Jing Yang, Yifan Zeng, Yunfei Liu, Meng Gao, Sen Liu, Zhengding Su & Yongqi Huang
Pages: 4883-4894
Published online: 19 Nov 2019
AbstractforElectrostatic interactions in molecular recognition of intrinsically disordered proteins | Full Text | References | PDF (2 MB) | EPUB
  • 1003 Views
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Letters to the Editor

Letter
Structural vaccinology approach to investigate the virulent and secretory proteins of Bacillus anthracis for devising anthrax next-generation vaccine
Nidhi Gupta, Nazia Khatoon, Amit Mishra, Vijay Kumar Verma & Vijay Kumar Prajapati
Pages: 4895-4905
Published online: 18 Nov 2019
AbstractforStructural vaccinology approach to investigate the virulent and secretory proteins of Bacillus anthracis for devising anthrax next-generation vaccine | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 181 Views
  • 8 CrossRef citations
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Letter
Impact of peripheral mutations on the access channels of human cytochrome P450 1A2
Beili Ying, Yang Zhong & Jingfang Wang
Pages: 4906-4913
Published online: 06 Nov 2019
AbstractforImpact of peripheral mutations on the access channels of human cytochrome P450 1A2 | Full Text | References | PDF (1.9 MB) | EPUB
  • 122 Views
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Letter
Inhibition of copper-induced aggregation of human γD-crystallin by a diimine molecule and investigations on their molecular interactions
Shiwani Rana, Anand Babu Velappan, Joy Debnath & Kalyan Sundar Ghosh
Pages: 4914-4920
Published online: 12 Nov 2019
AbstractforInhibition of copper-induced aggregation of human γD-crystallin by a diimine molecule and investigations on their molecular interactions | Full Text | References | PDF (997.8 KB) | EPUB | Supplemental
  • 128 Views
  • 7 CrossRef citations
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Letter
A proposed atomic model of the head-to-tail interaction in the filament structure of vimentin
Raja Dey & Peter Burkhard
Pages: 4921-4927
Published online: 13 Nov 2019
AbstractforA proposed atomic model of the head-to-tail interaction in the filament structure of vimentin | Full Text | References | PDF (1.4 MB) | EPUB
  • 232 Views
  • 1 CrossRef citations
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Letter
Structural assessment and identification of 11β-hydroxysteroid dehydrogenase type 1 inhibitors
Ananta Ganjoo, Anuj Tripathi & Prabhakar Chetti
Pages: 4928-4937
Published online: 13 Nov 2019
AbstractforStructural assessment and identification of 11β-hydroxysteroid dehydrogenase type 1 inhibitors | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 172 Views
  • 3 CrossRef citations
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Letter
Ligand-binding alters the mechanical stability of muscle protein titin domains
Hwanyoung Woo, Bumjoon Choi & Kilho Eom
Pages: 4938-4946
Published online: 13 Nov 2019
AbstractforLigand-binding alters the mechanical stability of muscle protein titin domains | Full Text | References | PDF (2.5 MB) | EPUB
  • 94 Views
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Letter
Pharmacophore modeling coupled with scaffold hopping to identify novel and potent ribosomal S6 kinase (RSK2) protein antagonists as anti-cancer agents
Praveen Kumar Guttula, Kirti Agrawal, Pradeep Natarajan & Mukesh Kumar Gupta
Pages: 4947-4955
Published online: 12 Nov 2019
AbstractforPharmacophore modeling coupled with scaffold hopping to identify novel and potent ribosomal S6 kinase (RSK2) protein antagonists as anti-cancer agents | Full Text | References | PDF (1.7 MB) | EPUB
  • 189 Views
  • 2 CrossRef citations
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Letter
Identification of potential soluble epoxide hydrolase (sEH) inhibitors by ligand-based pharmacophore model and biological evaluation
Sudha Bhagwati & Mohammad Imran Siddiqi
Pages: 4956-4966
Published online: 18 Nov 2019
AbstractforIdentification of potential soluble epoxide hydrolase (sEH) inhibitors by ligand-based pharmacophore model and biological evaluation | Full Text | References | PDF (3.1 MB) | EPUB
  • 325 Views
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Letter
Deciphering the interaction of food additive, vanillin with DNA: A biophysical and computational study
Faizan Abul Qais, Fohad Mabood Husain & Mohd Shahnawaz Khan
Pages: 4967-4975
Published online: 22 Nov 2019
AbstractforDeciphering the interaction of food additive, vanillin with DNA: A biophysical and computational study | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 125 Views
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