Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 8 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 8 (2021)

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Research Articles

Article
Targeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase
Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Ekampreet Singh, Amita Pathak, Rashmi Prabha Singh, Jayaraman Muthukumaran & Amit Kumar Singh
Pages: 2679-2692
Published online: 20 Apr 2020
AbstractforTargeting SARS-CoV-2: a systematic drug repurposing approach to identify promising inhibitors against 3C-like proteinase and 2′-O-ribose methyltransferase | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 11238 Views
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Article
A comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A)
Zoya Khalid & Osman Ugur Sezerman
Pages: 2693-2701
Published online: 20 Apr 2020
AbstractforA comprehensive study on identifying the structural and functional SNPs of human neuronal membrane glycoprotein M6A (GPM6A) | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 305 Views
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Article
Molecular modeling studies of benzothiophene-containing derivatives as promising selective estrogen receptor downregulators: a combination of 3D-QSAR, molecular docking and molecular dynamics simulations
Cuihua Zhang, Qunlin Li, Yujie Ren & Fei Liu
Pages: 2702-2723
Published online: 20 Apr 2020
AbstractforMolecular modeling studies of benzothiophene-containing derivatives as promising selective estrogen receptor downregulators: a combination of 3D-QSAR, molecular docking and molecular dynamics simulations | Full Text | References | PDF (4 MB) | EPUB
  • 199 Views
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Article
In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain)
Phulen Sarma, Nishant Shekhar, Manisha Prajapat, Pramod Avti, Hardeep Kaur, Subodh Kumar, Sanjay Singh, Harish Kumar, Ajay Prakash, Deba Prasad Dhibar & Bikash Medhi
Pages: 2724-2732
Published online: 18 May 2020
AbstractforIn-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain) | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 7170 Views
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Article
DeEPn: a deep neural network based tool for enzyme functional annotation
Rahul Semwal, Imlimaong Aier, Pankaj Tyagi & Pritish Kumar Varadwaj
Pages: 2733-2743
Published online: 22 Apr 2020
AbstractforDeEPn: a deep neural network based tool for enzyme functional annotation | Full Text | References | PDF (1.7 MB) | EPUB
  • 441 Views
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Article
Comparative analysis of the viscoelastic properties of collagen-like proteins by virtual creep test
Avrin Ghanaeian & Reza Soheilifard
Pages: 2744-2753
Published online: 20 Apr 2020
AbstractforComparative analysis of the viscoelastic properties of collagen-like proteins by virtual creep test | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 201 Views
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Article
Computational discovery of plant-based inhibitors against human carbonic anhydrase IX and molecular dynamics simulation
Shafi Mahmud, Ekhtiar Rahman, Zulkar Nain, Mutasim Billah, Sumon Karmakar, Sumon Chandro Mohanto, Gobindo Kumar Paul, Al Amin, Uzzal Kumar Acharjee & Md. Abu Saleh
Pages: 2754-2770
Published online: 29 Apr 2020
AbstractforComputational discovery of plant-based inhibitors against human carbonic anhydrase IX and molecular dynamics simulation | Full Text | References | PDF (3.3 MB) | EPUB
  • 432 Views
  • 13 CrossRef citations
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Article
Protein dynamics and molecular motions study in relation to molecular interaction between proteins from sulfur oxidizing proteobacteria Allochromatium vinosum
Semanti Ghosh & Angshuman Bagchi
Pages: 2771-2787
Published online: 06 May 2020
AbstractforProtein dynamics and molecular motions study in relation to molecular interaction between proteins from sulfur oxidizing proteobacteria Allochromatium vinosum | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 195 Views
  • 1 CrossRef citations
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Article
The binding process of BmKTX and BmKTX-D33H toward to Kv1.3 channel: a molecular dynamics simulation study
Qiancheng Zheng, Risong Na, Lianjuan Yang, Hui Yu, Xi Zhao & Xuri Huang
Pages: 2788-2797
Published online: 06 May 2020
AbstractforThe binding process of BmKTX and BmKTX-D33H toward to Kv1.3 channel: a molecular dynamics simulation study | Full Text | References | PDF (2.9 MB) | EPUB
  • 168 Views
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Article
Magnetite Fe3O4 surface as an effective drug delivery system for cancer treatment drugs: density functional theory study
Mahnaz Mohammadi & Fatematossadat Pourseyed Aghaei
Pages: 2798-2805
Published online: 21 Apr 2020
AbstractforMagnetite Fe3O4 surface as an effective drug delivery system for cancer treatment drugs: density functional theory study | Full Text | References | PDF (1.3 MB) | EPUB
  • 390 Views
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Article
Quantitative structure activity relationship and molecular simulations for the exploration of natural potent VEGFR-2 inhibitors: an in silico anti-angiogenic study
Neha Sharma, Mala Sharma, Qazi Inamur Rahman, Salman Akhtar & Mohd Muddassir
Pages: 2806-2823
Published online: 04 May 2020
AbstractforQuantitative structure activity relationship and molecular simulations for the exploration of natural potent VEGFR-2 inhibitors: an in silico anti-angiogenic study | Full Text | References | PDF (4.4 MB) | EPUB
  • 291 Views
  • 10 CrossRef citations
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Article
A series of molecular modeling techniques to reveal selective mechanisms of inhibitors to β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) and β-site amyloid precursor protein cleaving enzyme 2 (BACE2)
Shipeng Li, Hexiang Zhao, Jinghui Li, Jiajia Hao & Hualin Yu
Pages: 2824-2837
Published online: 20 Apr 2020
AbstractforA series of molecular modeling techniques to reveal selective mechanisms of inhibitors to β-Site amyloid precursor protein cleaving enzyme 1 (BACE1) and β-site amyloid precursor protein cleaving enzyme 2 (BACE2) | Full Text | References | PDF (4.1 MB) | EPUB
  • 306 Views
  • 6 CrossRef citations
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Article
BREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC)
Harun M. Patel, Matin Shaikh, Iqrar Ahmad, Deepak Lokwani & Sanjay J. Surana
Pages: 2838-2856
Published online: 23 Apr 2020
AbstractforBREED based de novo hybridization approach: generating novel T790M/C797S-EGFR tyrosine kinase inhibitors to overcome the problem of mutation and resistance in non small cell lung cancer (NSCLC) | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 323 Views
  • 20 CrossRef citations
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Article
Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study
Maryam Enayatkhani, Mehdi Hasaniazad, Sobhan Faezi, Hamed Gouklani, Parivash Davoodian, Nahid Ahmadi, Mohammad Ali Einakian, Afsaneh Karmostaji & Khadijeh Ahmadi
Pages: 2857-2872
Published online: 02 May 2020
AbstractforReverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study | Full Text | References | PDF (3.3 MB) | EPUB
  • 19048 Views
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Article
Molecular modelling and dynamic simulations of sequestosome 1 (SQSTM1) missense mutations linked to Paget disease of bone
Noor Ahmad Shaik, Khalidah K. Nasser, Muteb Muidh Alruwaili, Sami Raja Alallasi, Ramu Elango & Babajan Banaganapalli
Pages: 2873-2884
Published online: 13 May 2020
AbstractforMolecular modelling and dynamic simulations of sequestosome 1 (SQSTM1) missense mutations linked to Paget disease of bone | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 245 Views
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Article
Unique and exclusive peptide signatures directly identify intrinsically disordered proteins from sequences without structural information
Aditya Mittal, Anandkumar Madhavjibhai Changani & Sakshi Taparia
Pages: 2885-2893
Published online: 27 Apr 2020
AbstractforUnique and exclusive peptide signatures directly identify intrinsically disordered proteins from sequences without structural information | Full Text | References | PDF (1.2 MB) | EPUB | Supplemental
  • 467 Views
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Article
Tetrazolo[1,5-a]quinoline moiety-based Os(IV) complexes: DNA binding/cleavage, bacteriostatic and photocytotoxicity assay
Bharat H. Pursuwani, Bhupesh S. Bhatt, Foram U. Vaidya, Chandramani Pathak & Mohan N. Patel
Pages: 2894-2903
Published online: 29 Apr 2020
AbstractforTetrazolo[1,5-a]quinoline moiety-based Os(IV) complexes: DNA binding/cleavage, bacteriostatic and photocytotoxicity assay | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 127 Views
  • 7 CrossRef citations
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Article
Peptide-like and small-molecule inhibitors against Covid-19
Suyash Pant, Meenakshi Singh, V. Ravichandiran, U. S. N. Murty & Hemant Kumar Srivastava
Pages: 2904-2913
Published online: 06 May 2020
AbstractforPeptide-like and small-molecule inhibitors against Covid-19 | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 16550 Views
  • 207 CrossRef citations
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Article
Computational analysis of nuclear factor-κB and resveratrol in colorectal cancer
Begum Dariya, Santosh Kumar Behera, Gowru Srivani, Batoul Farran, Afroz Alam & Ganji Purnachandra Nagaraju
Pages: 2914-2922
Published online: 27 Apr 2020
AbstractforComputational analysis of nuclear factor-κB and resveratrol in colorectal cancer | Full Text | References | PDF (1.5 MB) | EPUB
  • 137 Views
  • 8 CrossRef citations
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Article
Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective
Abdo A. Elfiky & Eman B. Azzam
Pages: 2923-2931
Published online: 27 Apr 2020
AbstractforNovel guanosine derivatives against MERS CoV polymerase: An in silico perspective | Full Text | References | PDF (2.8 MB) | EPUB
  • 2793 Views
  • 41 CrossRef citations
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Article
Size-dependent dynamic stability analysis of the cantilevered curved microtubule-associated proteins (MAPs)
Pei Zhang, Zhenying Ge & Mehran Safarpour
Pages: 2932-2944
Published online: 05 May 2020
AbstractforSize-dependent dynamic stability analysis of the cantilevered curved microtubule-associated proteins (MAPs) | Full Text | References | PDF (2.7 MB) | EPUB
  • 154 Views
  • 3 CrossRef citations
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Article
Structure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors
Rohit Shukla, Harish Shukla & Timir Tripathi
Pages: 2945-2958
Published online: 30 Apr 2020
AbstractforStructure-based discovery of phenyl-diketo acids derivatives as Mycobacterium tuberculosis malate synthase inhibitors | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 280 Views
  • 13 CrossRef citations
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Article
Spectroscopic methodologies and computational simulation studies on the characterization of the interaction between human serum albumin and astragalin
ShaoLi Lyu & Wang Wang
Pages: 2959-2970
Published online: 29 Apr 2020
AbstractforSpectroscopic methodologies and computational simulation studies on the characterization of the interaction between human serum albumin and astragalin | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 186 Views
  • 17 CrossRef citations
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Article
Moroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations
I. Aanouz, A. Belhassan, K. El-Khatabi, T. Lakhlifi, M. El-ldrissi & M. Bouachrine
Pages: 2971-2979
Published online: 06 May 2020
AbstractforMoroccan Medicinal plants as inhibitors against SARS-CoV-2 main protease: Computational investigations | Full Text | References | PDF (1.4 MB) | EPUB
  • 14562 Views
  • 192 CrossRef citations
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Article
Drug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes
Ammar D. Elmezayen, Anas Al-Obaidi, Alp Tegin Şahin & Kemal Yelekçi
Pages: 2980-2992
Published online: 26 Apr 2020
AbstractforDrug repurposing for coronavirus (COVID-19): in silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes | Full Text | References | PDF (4.3 MB) | EPUB
  • 16876 Views
  • 171 CrossRef citations
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Article
New dehydroabietic acid (DHA) derivatives with anticancer activity against HepG2 cancer cell lines as a potential drug targeting EGFR kinase domain. CoMFA study and virtual ligand-based screening
Hanane Zaki, Assia Belhassan, Mohamed Benlyas, Tahar Lakhlifi & Mohammed Bouachrine
Pages: 2993-3003
Published online: 04 May 2020
AbstractforNew dehydroabietic acid (DHA) derivatives with anticancer activity against HepG2 cancer cell lines as a potential drug targeting EGFR kinase domain. CoMFA study and virtual ligand-based screening | Full Text | References | PDF (1.7 MB) | EPUB
  • 193 Views
  • 4 CrossRef citations
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Article
Structural insights into the Zika virus NS1 protein inhibition using a computational approach
Nasir Ahmad, Syed Lal Badshah, Muhammad Junaid, Ashfaq Ur Rehman, Akhtar Muhammad & Khalid Khan
Pages: 3004-3011
Published online: 06 May 2020
AbstractforStructural insights into the Zika virus NS1 protein inhibition using a computational approach | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 337 Views
  • 15 CrossRef citations
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Article
Bio-active mixed ligand Cu(II) and Zn(II) complexes of pyrimidine derivative Schiff base: DFT calculation, antimicrobial, antioxidant, DNA binding, anticancer and molecular docking studies
Nagaraj Revathi, Murugesan Sankarganesh, Jeyaraj Dhaveethu Raja, Gujuluva Gangatharan Vinoth Kumar, Arumugam Sakthivel & Ramalingam Rajasekaran
Pages: 3012-3024
Published online: 05 May 2020
AbstractforBio-active mixed ligand Cu(II) and Zn(II) complexes of pyrimidine derivative Schiff base: DFT calculation, antimicrobial, antioxidant, DNA binding, anticancer and molecular docking studies | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 496 Views
  • 29 CrossRef citations
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Review Articles

Review Article
A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin
Anwarul Hasan, Bilal Ahamad Paray, Arif Hussain, Fikry Ali Qadir, Farnoosh Attar, Falah Mohammad Aziz, Majid Sharifi, Hossein Derakhshankhah, Behnam Rasti, Masoumeh Mehrabi, Koorosh Shahpasand, Ali Akbar Saboury & Mojtaba Falahati
Pages: 3025-3033
Published online: 22 Apr 2020
AbstractforA review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin | Full Text | References | PDF (1.9 MB) | EPUB
  • 13386 Views
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Review Article
Dancing with Trojan horses: an interplay between the extracellular vesicles and viruses
Raied A. Badierah, Vladimir N. Uversky & Elrashdy M. Redwan
Pages: 3034-3060
Published online: 30 Apr 2020
AbstractforDancing with Trojan horses: an interplay between the extracellular vesicles and viruses | Full Text | References | PDF (3.2 MB) | EPUB
  • 1655 Views
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Correction

Correction
Correction
Page: i
Published online: 09 Apr 2021
CitationforCorrection | Full Text | PDF (101.1 KB) | EPUB
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