Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 9 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 9 (2020)

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Research Articles

Article
Investigating the reason for loss-of-function of Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) caused by Y279C mutation through molecular dynamics simulation
Wen-Shan Liu, Rui-Rui Wang, Wei-Ya Li, Mei Rong, Chi-Lu Liu, Ying Ma & Run-Ling Wang
Pages: 2509-2520
Published online: 01 Jul 2019
AbstractforInvestigating the reason for loss-of-function of Src homology 2 domain-containing protein tyrosine phosphatase 2 (SHP2) caused by Y279C mutation through molecular dynamics simulation | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 224 Views
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Article
Repurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis
Jyoti Rani, Yumnam Silla, Kasmika Borah, Srinivasan Ramachandran & Urmi Bajpai
Pages: 2521-2532
Published online: 11 Jul 2019
AbstractforRepurposing of FDA-approved drugs to target MurB and MurE enzymes in Mycobacterium tuberculosis | Full Text | References | PDF (3.1 MB) | EPUB
  • 526 Views
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Article
Identifying potential GluN2B subunit containing N-Methyl-D-aspartate receptor inhibitors: an integrative in silico and molecular modeling approach
Ravi Singh, Ankit Ganeshpurkar, Devendra Kumar, Dileep Kumar, Ashok Kumar & Sushil Kumar Singh
Pages: 2533-2545
Published online: 04 Jul 2019
AbstractforIdentifying potential GluN2B subunit containing N-Methyl-D-aspartate receptor inhibitors: an integrative in silico and molecular modeling approach | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 358 Views
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Article
Interaction, cytotoxicity and sustained release assessment of a novel anti-tumor agent using bovine serum albumin nanocarrier
Nassim Fattahian Kalhor, Maryam Saeidifar, Hassan Ramshini & Ali Akbar Saboury
Pages: 2546-2558
Published online: 09 Jul 2019
AbstractforInteraction, cytotoxicity and sustained release assessment of a novel anti-tumor agent using bovine serum albumin nanocarrier | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 201 Views
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Article
Protein–ligand interaction-guided discovery of novel VEGFR-2 inhibitors
Yanmin Zhang, Mingliang Zhang, Yuchen Wang, Yuanrong Fan, Xingye Chen, Yan Yang, Yi Hua, Wuchen Xie, Tao Lu, Weifang Tang, Yadong Chen & Haichun Liu
Pages: 2559-2574
Published online: 02 Jul 2019
AbstractforProtein–ligand interaction-guided discovery of novel VEGFR-2 inhibitors | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 522 Views
  • 11 CrossRef citations
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Article
Conformational change of a G-quadruplex under molecular crowding conditions
Ji Hoon Han, Ji Hoon Kim, Seog K. Kim & Yoon Jung Jang
Pages: 2575-2581
Published online: 15 Sep 2019
AbstractforConformational change of a G-quadruplex under molecular crowding conditions | Full Text | References | PDF (1.4 MB) | EPUB
  • 401 Views
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Article
Structure-activity relationship analysis of 3-phenylpyrazole derivatives as androgen receptor antagonists
Wenya Han & Jiazhong Li
Pages: 2582-2591
Published online: 05 Jul 2019
AbstractforStructure-activity relationship analysis of 3-phenylpyrazole derivatives as androgen receptor antagonists | Full Text | References | PDF (2.7 MB) | EPUB
  • 182 Views
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Article
Prediction and validation of HIV-1 gp41 ecto-transmembrane domain post-fusion trimeric structure using molecular modeling
Biswajit Gorai, Satyabrata Das & Prabal K. Maiti
Pages: 2592-2603
Published online: 02 Jul 2019
AbstractforPrediction and validation of HIV-1 gp41 ecto-transmembrane domain post-fusion trimeric structure using molecular modeling | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 209 Views
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Article
Exploring toxicity of perfluorinated compounds through complex network and pathway modeling
Xinhe Liu, Yu Zhu, Tingting Liu, Qiao Xue, Fang Tian, Yongna Yuan & Chunyan Zhao
Pages: 2604-2612
Published online: 08 Jul 2019
AbstractforExploring toxicity of perfluorinated compounds through complex network and pathway modeling | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 483 Views
  • 6 CrossRef citations
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Article
Modulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation
Likun Zhao, Yanhua Ouyang, Qian Li & Zhuqing Zhang
Pages: 2613-2623
Published online: 08 Jul 2019
AbstractforModulation of p53 N-terminal transactivation domain 2 conformation ensemble and kinetics by phosphorylation | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 363 Views
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Article
Allosteric activation of metabotropic glutamate receptor 5
Balázs Jójárt, Zoltán Orgován, Árpád Márki, Gáspár Pándy-Szekeres, György G. Ferenczy & György M. Keserű
Pages: 2624-2632
Published online: 17 Jul 2019
AbstractforAllosteric activation of metabotropic glutamate receptor 5 | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 2015 Views
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Open Access
Article
Functional study of 14-3-3 protein epsilon (YWHAE) in keratinocytes: microarray integrating bioinformatics approaches
Shang-Jun Yin, Jae-Rin Lee, Hyunchang Kwak, Bit-Na Lee, Ji-Won Han, Myong-Joon Hahn, Yong-Doo Park & Jun-Mo Yang
Pages: 2633-2649
Published online: 05 Jul 2019
AbstractforFunctional study of 14-3-3 protein epsilon (YWHAE) in keratinocytes: microarray integrating bioinformatics approaches | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 369 Views
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Article
Spectroscopic and molecular docking studies on interaction of two Schiff base complexes with bovine serum albumin
Hamid Dezhampanah, Masoomeh Esmaili & Shabnam Jampour
Pages: 2650-2658
Published online: 15 Jul 2019
AbstractforSpectroscopic and molecular docking studies on interaction of two Schiff base complexes with bovine serum albumin | Full Text | References | PDF (2 MB) | EPUB
  • 238 Views
  • 9 CrossRef citations
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Article
Interaction of piroxicam with bovine serum albumin investigated by spectroscopic, calorimetric and computational molecular methods
Ludmila Aricov, Daniel George Angelescu, Adriana Băran, Anca Ruxandra Leontieş, Vlad Tudor Popa, Aurica Precupaş, Romică Sandu, Gabriela Stîngă & Dan-Florin Anghel
Pages: 2659-2671
Published online: 29 Jul 2019
AbstractforInteraction of piroxicam with bovine serum albumin investigated by spectroscopic, calorimetric and computational molecular methods | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 217 Views
  • 13 CrossRef citations
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Article
Virtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies
Ya-Ya Liu, Xiao-Yan Feng, Wen-Qing Jia, Zhi Jing, Wei-Ren Xu & Xian-Chao Cheng
Pages: 2672-2685
Published online: 11 Sep 2019
AbstractforVirtual identification of novel PPARα/γ dual agonists by 3D-QSAR, molecule docking and molecular dynamics studies | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 286 Views
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Article
Binding mode of a cationic porphyrin to parallel and antiparallel thrombin binding aptamer G-quadruplex
Ha Young Cho, Young-Ae Lee, Ye Sol Oh, Gil Jun Lee, Yoon Jung Jang & Seog K. Kim
Pages: 2686-2692
Published online: 08 Aug 2019
AbstractforBinding mode of a cationic porphyrin to parallel and antiparallel thrombin binding aptamer G-quadruplex | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 288 Views
  • 3 CrossRef citations
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Article
Biomolecular interaction of a platelet aggregation inhibitor, 3,4-methylenedioxy-β-nitrostyrene with human serum albumin: multi-spectral and computational characterization
Md. Zahirul Kabir, Amira Adlin Roslan, Nor Farrah Wahidah Ridzwan, Saharuddin B. Mohamad & Saad Tayyab
Pages: 2693-2703
Published online: 15 Jul 2019
AbstractforBiomolecular interaction of a platelet aggregation inhibitor, 3,4-methylenedioxy-β-nitrostyrene with human serum albumin: multi-spectral and computational characterization | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 176 Views
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Article
A profound computational study to prioritize the natural compound inhibitors against the P. falciparum orotidine-5-monophosphate decarboxylase enzyme
Anu Manhas, Saikat Dubey & Prakash C. Jha
Pages: 2704-2716
Published online: 22 Jul 2019
AbstractforA profound computational study to prioritize the natural compound inhibitors against the P. falciparum orotidine-5-monophosphate decarboxylase enzyme | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 186 Views
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Article
Potential of isoquercitrin as antisickling agent: a multi-spectroscopic, thermophoresis and molecular modeling approach
Muntjeeb M. Syed, Pooja. J. Doshi, Dilip D. Dhavale, Jignesh B. Doshi, Sudam L. Kate, Girish Kulkarni, Neeru Sharma, Mallikarjunachari Uppuladinne, Uddhavesh Sonavane, Rajendra Joshi & Mohan. V. Kulkarni
Pages: 2717-2736
Published online: 01 Aug 2019
AbstractforPotential of isoquercitrin as antisickling agent: a multi-spectroscopic, thermophoresis and molecular modeling approach | Full Text | References | PDF (4.3 MB) | EPUB
  • 254 Views
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Article
Understanding co-loading of doxorubicin and camptothecin on graphene and folic acid-conjugated graphene for targeting drug delivery: classical MD simulation and DFT calculation
Abutaleb Alinejad, Heidar Raissi & Hassan Hashemzadeh
Pages: 2737-2745
Published online: 26 Jul 2019
AbstractforUnderstanding co-loading of doxorubicin and camptothecin on graphene and folic acid-conjugated graphene for targeting drug delivery: classical MD simulation and DFT calculation | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 606 Views
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Review Article

Review Article
Strategies of enzyme immobilization on nanomatrix supports and their intracellular delivery
Majid Sharifi, Abdulkarim Yasin Karim, Nadir Mustafa Qadir Nanakali, Abbas Salihi, Falah Mohammad Aziz, Jun Hong, Rizwan Hasan Khan, Ali Akbar Saboury, Anwarul Hasan, Osama K. Abou-Zied & Mojtaba Falahati
Pages: 2746-2762
Published online: 22 Jul 2019
AbstractforStrategies of enzyme immobilization on nanomatrix supports and their intracellular delivery | Full Text | References | PDF (3 MB) | EPUB
  • 761 Views
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Letters to the Editor

Letter
Can a retro-polypeptide fold into a globule?
Victor P. Kutyshenko, Mars G. Sharapov & Vladimir N. Uversky
Pages: 2763-2767
Published online: 02 Jul 2019
AbstractforCan a retro-polypeptide fold into a globule? | Full Text | References | PDF (1 MB) | EPUB
  • 76 Views
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Letter
Insight derived from molecular dynamics simulation into cold-adaptation mechanism of trypsins
Li-Quan Yang, Yi-Rui Yin, Jian-Xin Shen, Yi Li, Shu-Qun Liu & Peng Sang
Pages: 2768-2776
Published online: 01 Jul 2019
AbstractforInsight derived from molecular dynamics simulation into cold-adaptation mechanism of trypsins | Full Text | References | PDF (1.7 MB) | EPUB
  • 124 Views
  • 2 CrossRef citations
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Letter
Complexation of cis-Pt and trans-Pt(NH3)2Cl2 with serum proteins: A potential application for drug delivery
P. Chanphai, J. Bariyanga, G. Bérubé & H. A. Tajmir-Riahi
Pages: 2777-2783
Published online: 22 Aug 2019
AbstractforComplexation of cis-Pt and trans-Pt(NH3)2Cl2 with serum proteins: A potential application for drug delivery | Full Text | References | PDF (1.5 MB) | EPUB
  • 166 Views
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Letter
Regulation mechanism of lysC riboswitch in gram-positive bacterium Bacillus subtilis
Yuying Sun, Yanli Wang, Zhi-Jie Tan & Wenbing Zhang
Pages: 2784-2791
Published online: 17 Jul 2019
AbstractforRegulation mechanism of lysC riboswitch in gram-positive bacterium Bacillus subtilis | Full Text | References | PDF (1.9 MB) | EPUB
  • 251 Views
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Letter
Spectroscopic methods and in silico analyses using density functional theory to characterize and identify piperine alkaloid crystals isolated from pepper (Piper Nigrum L.)
Fabrine Silva Alves, José de Arimatéia Rodrigues Do Rego, Marcondes Lima Da Costa, Luiz Fernando Lobato Da Silva, Renato Araújo Da Costa, Jorddy Neves Cruz & Davi Do Socorro Barros Brasil
Pages: 2792-2799
Published online: 15 Jul 2019
AbstractforSpectroscopic methods and in silico analyses using density functional theory to characterize and identify piperine alkaloid crystals isolated from pepper (Piper Nigrum L.) | Full Text | References | PDF (1.5 MB) | EPUB
  • 314 Views
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Letter
Ligand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors
Ramar Vanajothi, Vedagiri Hemamalini, Jeyaraman Jeyakanthan & Kumpati Premkumar
Pages: 2800-2808
Published online: 08 Aug 2019
AbstractforLigand-based pharmacophore mapping and virtual screening for identification of potential discoidin domain receptor 1 inhibitors | Full Text | References | PDF (1.4 MB) | EPUB
  • 373 Views
  • 17 CrossRef citations
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Letter
A molecular modeling study of components of the ginger (Zingiber officinale) extract inside human butyrylcholinesterase: implications for Alzheimer disease
Teobaldo Cuya & Tanos Celmar Costa França
Pages: 2809-2815
Published online: 22 Jul 2019
First Page PreviewforA molecular modeling study of components of the ginger (Zingiber officinale) extract inside human butyrylcholinesterase: implications for Alzheimer disease | Full Text | References | PDF (1.9 MB) | EPUB
  • 138 Views
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Retractions

Retraction
Statement of Retraction: Protein blueprint and their interactions while approachability struggle for amino acids
Page: i
Published online: 13 May 2020
CitationforStatement of Retraction: Protein blueprint and their interactions while approachability struggle for amino acids | Full Text | PDF (94.8 KB) | EPUB
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