Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 13 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 13 (2020)

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Research Articles

Article
Structural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors
Bhavya Somalapura Gangadharappa, Rajashekarappa Sharath, Prasanna D. Revanasiddappa, Vivek Chandramohan, Meenakshisundaram Balasubramaniam & Teja Priya Vardhineni
Pages: 3757-3771
Published online: 23 Sep 2019
AbstractforStructural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors | Full Text | References | PDF (3.5 MB) | EPUB
  • 790 Views
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Article
Hit identification and drug repositioning of potential non-nucleoside reverse transcriptase inhibitors by structure-based approach using computational tools (part II)
Pretisha Flora Cutinho, Ravi C. Shankar, Avinash Anand, Jaydeep Roy, Chetan H. Mehta, Usha Y. Nayak & Manikanta Murahari
Pages: 3772-3789
Published online: 17 Sep 2019
AbstractforHit identification and drug repositioning of potential non-nucleoside reverse transcriptase inhibitors by structure-based approach using computational tools (part II) | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 251 Views
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Article
The guanidiniocarbonylpyrrole–fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition
Mirsada Ćehić, Josipa Suć Sajko, Zrinka Karačić, Patryciusz Piotrowski, Tamara Šmidlehner, Ivanka Jerić, Carsten Schmuck, Ivo Piantanida & Sanja Tomić
Pages: 3790-3800
Published online: 25 Sep 2019
AbstractforThe guanidiniocarbonylpyrrole–fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 283 Views
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Article
Formation of the inclusion complex of water soluble fluorescent calix[4]arene and naringenin: solubility, cytotoxic effect and molecular modeling studies
Mehmet Oguz, Asif Ali Bhatti, Berna Dogan, Serdar Karakurt, Serdar Durdagi & Mustafa Yilmaz
Pages: 3801-3813
Published online: 11 Oct 2019
AbstractforFormation of the inclusion complex of water soluble fluorescent calix[4]arene and naringenin: solubility, cytotoxic effect and molecular modeling studies | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 614 Views
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Article
Design, synthesis, biological evaluation and molecular dynamics studies of 4-thiazolinone derivatives as protein tyrosine phosphatase 1B (PTP1B) inhibitors
Wen-Shan Liu, Rui-Rui Wang, Hai Yue, Zhi-Hui Zheng, Xin-Hua Lu, Shu-Qing Wang, Wei-Li Dong & Run-Ling Wang
Pages: 3814-3824
Published online: 19 Sep 2019
AbstractforDesign, synthesis, biological evaluation and molecular dynamics studies of 4-thiazolinone derivatives as protein tyrosine phosphatase 1B (PTP1B) inhibitors | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 346 Views
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Article
Precise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation
Yuan Su, Peilu Song, Hanxun Wang, Baichun Hu, Jian Wang & Mao-Sheng Cheng
Pages: 3825-3837
Published online: 15 Sep 2019
AbstractforPrecise design of highly isoform-selective p21-activated kinase 4 inhibitors: computational insights into the selectivity mechanism through molecular dynamics simulation and binding free energy calculation | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 218 Views
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Article
An integrated computational approach to identify GC minor groove binders using various molecular docking scoring functions, dynamics simulations and binding free energy calculations
Mehul N. Soni, Sivakumar Prasanth Kumar, Kaid Johar S. R.Rakesh M. Rawal & Himanshu A. Pandya
Pages: 3838-3855
Published online: 08 Oct 2019
AbstractforAn integrated computational approach to identify GC minor groove binders using various molecular docking scoring functions, dynamics simulations and binding free energy calculations | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 210 Views
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Article
Structural insights into the interactions of flavin mononucleotide (FMN) and riboflavin with FMN riboswitch: a molecular dynamics simulation study
Padmaja D. Wakchaure, Kalyanashis Jana & Bishwajit Ganguly
Pages: 3856-3866
Published online: 15 Sep 2019
AbstractforStructural insights into the interactions of flavin mononucleotide (FMN) and riboflavin with FMN riboswitch: a molecular dynamics simulation study | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 417 Views
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Article
Insights into the interaction mechanisms of estrogen-related receptor alpha (ERRα) with ligands via molecular dynamics simulations
Dongping Li, Yingchun Cai, Dan Teng, Zengrui Wu, Weihua Li, Yun Tang & Guixia Liu
Pages: 3867-3878
Published online: 16 Sep 2019
AbstractforInsights into the interaction mechanisms of estrogen-related receptor alpha (ERRα) with ligands via molecular dynamics simulations | Full Text | References | PDF (3 MB) | EPUB
  • 219 Views
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Article
Designing new generation of potent inhibitors against membrane-type matrix metalloproteinase-2: a computational effort against multiple myeloma
Shohreh Fakhari, Azzurra Stefanucci, Adriano Mollica, Bahram Nikkhoo, Elham Tafsiri, Ali Jalili & Sako Mirzaie
Pages: 3879-3891
Published online: 16 Oct 2019
AbstractforDesigning new generation of potent inhibitors against membrane-type matrix metalloproteinase-2: a computational effort against multiple myeloma | Full Text | References | PDF (3.7 MB) | EPUB
  • 171 Views
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Article
Evaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer’s disease
Ahmad Abu Turab Naqvi, Deeba Shamim Jairajpuri, Omar Mohammed Ali Noman, Afzal Hussain, Asimul Islam, Faizan Ahmad, Mohammed F. Alajmi & Md. Imtaiyaz Hassan
Pages: 3892-3907
Published online: 25 Sep 2019
AbstractforEvaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer’s disease | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 355 Views
  • 30 CrossRef citations
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Article
Aminoacid substitutions in the glycine zipper affect the conformational stability of amyloid beta fibrils
Gianvito Grasso, Luigi Leanza, Umberto Morbiducci, Andrea Danani & Marco A. Deriu
Pages: 3908-3915
Published online: 07 Oct 2019
AbstractforAminoacid substitutions in the glycine zipper affect the conformational stability of amyloid beta fibrils | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 288 Views
  • 8 CrossRef citations
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Article
Interaction of saffron carotenoids with catalase: in vitro, in vivo and molecular docking studies
S. Ali Hashemi, S. Zahra Bathaie & Mohammad-Ali Mohagheghi
Pages: 3916-3926
Published online: 27 Sep 2019
AbstractforInteraction of saffron carotenoids with catalase: in vitro, in vivo and molecular docking studies | Full Text | References | PDF (1.9 MB) | EPUB
  • 259 Views
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Article
In silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis
Simranjeet Singh Narang, Suniba Shuaib, Deepti Goyal & Bhupesh Goyal
Pages: 3927-3941
Published online: 27 Sep 2019
AbstractforIn silico-guided identification of potential inhibitors against β2m aggregation in dialysis-related amyloidosis | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 250 Views
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Article
How oncogenic mutations activate human MAP kinase 1 (MEK1): a molecular dynamics simulation study
Ye Liu, Jingxuan Zhu, Xiaoqing Guo, Tianci Huang, Jiarui Han, Jianjiong Gao, Dong Xu & Weiwei Han
Pages: 3942-3958
Published online: 06 Nov 2019
AbstractforHow oncogenic mutations activate human MAP kinase 1 (MEK1): a molecular dynamics simulation study | Full Text | References | PDF (6.5 MB) | EPUB | Supplemental
  • 247 Views
  • 6 CrossRef citations
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Article
Ribonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection
Vasily N. Danilevich, Sergey A. Kozlov, Taras V. Shevchuk, Vladimir A. Oleinikov, Svetlana V. Sizova, Yuriy M. Khodarovich & Andrey L. Mulyukin
Pages: 3959-3971
Published online: 27 Sep 2019
AbstractforRibonucleic acid (RNA) condensation by thermal cycling with metal cations: yield of nanoparticles and their applicability for transfection | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 185 Views
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Article
Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach
Hema Sree G. N. S, Saraswathy Ganesan Rajalekshmi, Manikanta Murahari & Raghunadha R. Burri
Pages: 3972-3989
Published online: 14 Oct 2019
AbstractforReappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach | Full Text | References | PDF (5.6 MB) | EPUB | Supplemental
  • 425 Views
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Article
Rv0807, a putative phospholipase A2 of Mycobacterium tuberculosis; Elucidation through sequence analysis, homology modeling, molecular docking and molecular dynamics studies of potential substrates and inhibitors
Shobana Sundar, Lokesh Thangamani, Gowdham Manivel, Praveen Kumar & Shanmughavel Piramanayagam
Pages: 3990-4004
Published online: 24 Oct 2019
AbstractforRv0807, a putative phospholipase A2 of Mycobacterium tuberculosis; Elucidation through sequence analysis, homology modeling, molecular docking and molecular dynamics studies of potential substrates and inhibitors | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 187 Views
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Letters to the Editor

Letter
Identification of potential cruzain inhibitors using de novo design, molecular docking and dynamics simulations studies
Shovonlal Bhowmick, Rekha Dhondiram Chorge, Chaitanya Sadashiv Jangam, Lomate Dhanraj Bharatrao, Pritee Chunarkar Patil, Rupesh V. Chikhale & Md. Ataul Islam
Pages: 4005-4015
Published online: 13 Sep 2019
AbstractforIdentification of potential cruzain inhibitors using de novo design, molecular docking and dynamics simulations studies | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 376 Views
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Letter
Molecular dynamics simulations reveal the determinants of cyclin-dependent kinase 2 inhibition by 5-nitrosopyrimidine derivatives
Stefano Guglielmo, Daniela Cortese, Celine Cano & Roberta Fruttero
Pages: 4016-4024
Published online: 23 Sep 2019
AbstractforMolecular dynamics simulations reveal the determinants of cyclin-dependent kinase 2 inhibition by 5-nitrosopyrimidine derivatives | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 155 Views
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Letter
Effect of berberine hydrochloride-functionalized gold nanoparticles on calf thymus DNA: a biophysical study
Yong-Chang Liu, Cheng Xu, Wen-Wen Ren, Yi Ke, Ai-Min Bai & Yan-Jun Hu
Pages: 4025-4031
Published online: 31 Oct 2019
AbstractforEffect of berberine hydrochloride-functionalized gold nanoparticles on calf thymus DNA: a biophysical study | Full Text | References | PDF (1.7 MB) | EPUB
  • 182 Views
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Letter
Exploring the structural interaction of BSA with amine functionalized ruthenium(II) metal complex
Athanas Anish Babu, Kamaraj Karthick, Ramasamy Subramanian & Kalaiyar Swarnalatha
Pages: 4032-4039
Published online: 01 Nov 2019
AbstractforExploring the structural interaction of BSA with amine functionalized ruthenium(II) metal complex | Full Text | References | PDF (1.9 MB) | EPUB
  • 141 Views
  • 4 CrossRef citations
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Letter
Exploring the allosteric mechanism of protein tyrosine phosphatase 1B by molecular dynamics simulations
Quan Wang, Xue-Qi Fu & Qing-Chuan Zheng
Pages: 4040-4047
Published online: 25 Oct 2019
AbstractforExploring the allosteric mechanism of protein tyrosine phosphatase 1B by molecular dynamics simulations | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 175 Views
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Letter
Why double-stranded RNA with 5′-monophosphate is a poor binder to retinoic acid-inducible gene-I with respect to 5′-hydroxyl analogue?
Amit Kumar & Priyadarshi Satpati
Pages: 4048-4055
Published online: 04 Oct 2019
AbstractforWhy double-stranded RNA with 5′-monophosphate is a poor binder to retinoic acid-inducible gene-I with respect to 5′-hydroxyl analogue? | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 227 Views
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Letter
Unravelling the interaction of a phosphodiesterase inhibitor, aminophylline with human serum albumin: implication of photoilluminated riboflavin upon binding
Saniyya Khan & Imrana Naseem
Pages: 4056-4065
Published online: 30 Sep 2019
First Page PreviewforUnravelling the interaction of a phosphodiesterase inhibitor, aminophylline with human serum albumin: implication of photoilluminated riboflavin upon binding | Full Text | References | PDF (2.1 MB) | EPUB
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Correction

Correction
Correction notice
Page: i
Published online: 07 Jul 2020
CitationforCorrection notice | Full Text | PDF (93.3 KB) | EPUB
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