Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 16 (2019)

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Journal of Biomolecular Structure and Dynamics, Volume 37, Issue 16 (2019)

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Research Article

Article
Location of multiple binding sites for testo and testo–Pt(II) with tRNA
P. Chanphai, V. Ouellette, S. Mandal, S. K. Mandal, G. Bérubé & H. A. Tajmir-Riahi
Pages: 4133-4139
Published online: 24 Dec 2018
AbstractforLocation of multiple binding sites for testo and testo–Pt(II) with tRNA | Full Text | References | PDF (1.3 MB) | EPUB
  • 183 Views
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Letter to the Editor

Letter
TEF 2.0: a graph-based method for decomposing protein structures into closed loops
Dirk Stratmann, Jananan S. Pathmanathan, Guillaume Postic, Julien Rey & Jacques Chomilier
Pages: 4140-4150
Published online: 25 Dec 2018
First Page PreviewforTEF 2.0: a graph-based method for decomposing protein structures into closed loops | Full Text | References | PDF (2 MB) | EPUB
  • 112 Views
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Research Article

Article
Comparing protein structures and inferring functions with a novel three-dimensional Yau–Hausdorff method
Kun Tian, Xin Zhao, Yuning Zhang & Stephen Yau
Pages: 4151-4160
Published online: 05 Dec 2018
AbstractforComparing protein structures and inferring functions with a novel three-dimensional Yau–Hausdorff method | Full Text | References | PDF (1.5 MB) | EPUB
  • 299 Views
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Article
Comparative study of the binding mode between cytochrome P450 17A1 and prostate cancer drugs in the absence of haem iron
Dalong Song, Jihua Zhang, Yuanlin Wang, Jianxin Hu, Shuxiong Xu, Yuangao Xu, Hujun Shen, Xiaopeng Wen & Zhaolin Sun
Pages: 4161-4170
Published online: 11 Jan 2019
AbstractforComparative study of the binding mode between cytochrome P450 17A1 and prostate cancer drugs in the absence of haem iron | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 212 Views
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Letter to the Editor

Letter
Computational design, structure refinement and molecular dynamics simulation of novel engineered serratiopeptidase analogs
Maryam Rouhani, Vahideh Valizadeh, Reza Ahangari Cohan & Dariush Norouzian
Pages: 4171-4180
Published online: 18 Nov 2018
AbstractforComputational design, structure refinement and molecular dynamics simulation of novel engineered serratiopeptidase analogs | Full Text | References | PDF (3.6 MB) | EPUB
  • 190 Views
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Research Article

Article
Multicomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors
Anu Manhas, Mohsin Y. Lone & Prakash C. Jha
Pages: 4181-4199
Published online: 16 Jan 2019
AbstractforMulticomplex-based pharmacophore modeling in conjunction with multi-target docking and molecular dynamics simulations for the identification of PfDHFR inhibitors | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 263 Views
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Article
Identifying the novel inhibitors of lysine-specific demethylase 1 (LSD1) combining pharmacophore-based and structure-based virtual screening
Xu-Dong Sun, Yi-Chao Zheng, Chao-Ya Ma, Jing Yang, Qi-Bing Gao, Ying Yan, Zhi-Zheng Wang, Wen Li, Wen Zhao, Hong-Min Liu & Lina Ding
Pages: 4200-4214
Published online: 05 Dec 2018
AbstractforIdentifying the novel inhibitors of lysine-specific demethylase 1 (LSD1) combining pharmacophore-based and structure-based virtual screening | Full Text | References | PDF (3.1 MB) | EPUB
  • 257 Views
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Article
A coarse-grain MD (molecular dynamic) simulation of PCL–PEG and PLA–PEG aggregation as a computational model for prediction of the drug-loading efficacy of doxorubicin
Seyed Mohammad Ebrahim Kamrani & Farzin Hadizadeh
Pages: 4215-4221
Published online: 10 Jan 2019
AbstractforA coarse-grain MD (molecular dynamic) simulation of PCL–PEG and PLA–PEG aggregation as a computational model for prediction of the drug-loading efficacy of doxorubicin | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 461 Views
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Article
Identification of new promising plant-based lead compounds for inhibition of prokaryotic replicative DNA polymerases: combination of in silico and in vitro studies
Milad Lagzian, Ali Qasemi, Pegah Kaviani & Malihe Mohammadi
Pages: 4222-4237
Published online: 10 Dec 2018
AbstractforIdentification of new promising plant-based lead compounds for inhibition of prokaryotic replicative DNA polymerases: combination of in silico and in vitro studies | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 131 Views
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Article
Synthesis of new ultrasonic-assisted palladium oxide nanoparticles: an in vitro evaluation on cytotoxicity and DNA/BSA binding properties
Ziba Sorinezami, Hassan Mansouri-Torshizi, Mohammad Aminzadeh, Arezou Ghahghaei, Nasimeh Jamgohari & Mostafa Heidari Majd
Pages: 4238-4250
Published online: 02 Jan 2019
AbstractforSynthesis of new ultrasonic-assisted palladium oxide nanoparticles: an in vitro evaluation on cytotoxicity and DNA/BSA binding properties | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 261 Views
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Letter to the Editor

Letter
Study of interaction between citrate-coated silver nanoparticles and gamma globulin using spectroscopic method
Wanju Zhang, Kai Zhang, Xujie Xiong & Yanmei Chen
Pages: 4251-4257
Published online: 16 Jan 2019
AbstractforStudy of interaction between citrate-coated silver nanoparticles and gamma globulin using spectroscopic method | Full Text | References | PDF (893.4 KB) | EPUB | Supplemental
  • 254 Views
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Letter
Does the peptide backbone unit interact with gold nanoclusters? Insights from computational modeling
Mohamed Taha & Ming-Jer Lee
Pages: 4258-4266
Published online: 28 Dec 2018
AbstractforDoes the peptide backbone unit interact with gold nanoclusters? Insights from computational modeling | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 122 Views
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Letter
Calcium-doped single-wall nanotubes (Ca/SWCNTs) as a superior carrier for atropine drug delivery: a quantum-chemical study in gas and solvent phases
Mitra Mirmotahari, Emad Sani, Ali Shokuhi Rad & Mohammad A. Khalilzadeh
Pages: 4267-4273
Published online: 29 Dec 2018
AbstractforCalcium-doped single-wall nanotubes (Ca/SWCNTs) as a superior carrier for atropine drug delivery: a quantum-chemical study in gas and solvent phases | Full Text | References | PDF (1.4 MB) | EPUB
  • 136 Views
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Express Communication

Article
Prediction, docking study and molecular simulation of 3D DNA aptamers to their targets of endocrine disrupting chemicals
Weiwen Zhang, Fengxiao Yang, Dejin Ou, Ge Lin, Aiyun Huang, Nan Liu & Pinle Li
Pages: 4274-4282
Published online: 10 Jan 2019
AbstractforPrediction, docking study and molecular simulation of 3D DNA aptamers to their targets of endocrine disrupting chemicals | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 890 Views
  • 10 CrossRef citations
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Letter to the Editor

Letter
Study on the interaction of amprolium HCl and dinitolmide in animal-derived food products with BSA by multiple spectroscopies and molecular modeling techniques
Xiao-yue Sun, Shu-yun Bi, Jun Wu & Rui Zhao
Pages: 4283-4291
Published online: 13 Jan 2019
AbstractforStudy on the interaction of amprolium HCl and dinitolmide in animal-derived food products with BSA by multiple spectroscopies and molecular modeling techniques | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 95 Views
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Letter
New insights into the binding interaction of food protein ovalbumin with malachite green dye by hybrid spectroscopic and molecular docking analysis
Ramar Rajamanikandan, Arumugam Selva Sharma & Malaichamy Ilanchelian
Pages: 4292-4300
Published online: 11 Jan 2019
AbstractforNew insights into the binding interaction of food protein ovalbumin with malachite green dye by hybrid spectroscopic and molecular docking analysis | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 209 Views
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Research Article

Article
In silico hit optimization toward AKT inhibition: fragment-based approach, molecular docking and molecular dynamics study
Elkin Eduardo Sanabria-Chanaga, Irene Betancourt-Conde, Alicia Hernández-Campos, Alfredo Téllez-Valencia & Rafael Castillo
Pages: 4301-4311
Published online: 29 Jan 2019
AbstractforIn silico hit optimization toward AKT inhibition: fragment-based approach, molecular docking and molecular dynamics study | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 410 Views
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Article
Identification of novel urease inhibitors: pharmacophore modeling, virtual screening and molecular docking studies
Richa Arora, Upasana Issar & Rita Kakkar
Pages: 4312-4326
Published online: 24 Dec 2018
AbstractforIdentification of novel urease inhibitors: pharmacophore modeling, virtual screening and molecular docking studies | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 377 Views
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Article
Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: a comparative docking and MD simulation studies
Mehak Gulzar, Shahid Ali, Faez Iqbal Khan, Parvez Khan, Pankaj Taneja & Md. Imtaiyaz Hassan
Pages: 4327-4337
Published online: 11 Jan 2019
AbstractforBinding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: a comparative docking and MD simulation studies | Full Text | References | PDF (2.7 MB) | EPUB
  • 504 Views
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Letter to the Editor

Letter
Interaction of anticancer drug pinostrobin with lysozyme: a biophysical and molecular docking approach
Masihuz Zaman, Haaris Ahsan Safdari, Asra Nasir Khan, Syed Mohammad Zakariya, Saima Nusrat, Tajalli Ilm Chandel & Rizwan Hasan Khan
Pages: 4338-4344
Published online: 09 Jan 2019
AbstractforInteraction of anticancer drug pinostrobin with lysozyme: a biophysical and molecular docking approach | Full Text | References | PDF (1.2 MB) | EPUB
  • 303 Views
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Research Article

Article
Design of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics
Sukrit Srivastava, Mohit Kamthania, Rajesh Kumar Pandey, Ajay Kumar Saxena, Vaishali Saxena, Santosh Kumar Singh, Rakesh Kumar Sharma & Nishi Sharma
Pages: 4345-4360
Published online: 16 Jan 2019
AbstractforDesign of novel multi-epitope vaccines against severe acute respiratory syndrome validated through multistage molecular interaction and dynamics | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 1359 Views
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Article
Molecular dynamics analysis of the effects of GTP, GDP and benzimidazole derivative on structural dynamics of a cell division protein FtsZ from Mycobacterium tuberculosis
Supriya Hakeem, Inderpal Singh, Preeti Sharma, Anshul Uppal, Yugal Khajuria, Vijeshwar Verma, Vladimir N. Uversky & Ratna Chandra
Pages: 4361-4373
Published online: 11 Jan 2019
AbstractforMolecular dynamics analysis of the effects of GTP, GDP and benzimidazole derivative on structural dynamics of a cell division protein FtsZ from Mycobacterium tuberculosis | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 391 Views
  • 9 CrossRef citations
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Article
Computational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding
Clauber Henrique Souza Costa, Amanda Ruslana Santana Oliveira, Alberto M. dos Santos, Kauê Santana da Costa, Anderson Henrique Lima e Lima, Cláudio N. Alves & Jerônimo Lameira
Pages: 4374-4383
Published online: 28 Jan 2019
AbstractforComputational study of conformational changes in human 3-hydroxy-3-methylglutaryl coenzyme reductase induced by substrate binding | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 328 Views
  • 12 CrossRef citations
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Article
Insight into binding mechanisms of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations
Shanhe Wan, Ruohong Yan, Ying Jiang, Zhonghuang Li, Jiajie Zhang & Xiaoyun Wu
Pages: 4384-4394
Published online: 11 Jan 2019
AbstractforInsight into binding mechanisms of EGFR allosteric inhibitors using molecular dynamics simulations and free energy calculations | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 588 Views
  • 18 CrossRef citations
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Article
Thiophenacetamide as a potential modulator to NF-κB: structure and dynamics study using in silico and molecular biology assays
Vanessa S. Silva, Fatima M. Vergara, Leonardo N. Seito, Deborah Antunes, Lucianna H. S. Santos, Maria G. Henriques & Ernesto R. Caffarena
Pages: 4395-4406
Published online: 11 Jan 2019
AbstractforThiophenacetamide as a potential modulator to NF-κB: structure and dynamics study using in silico and molecular biology assays | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 168 Views
  • 3 CrossRef citations
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