Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 11 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 11 (2020)

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Research Articles

Article
Structure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections
Anupriya Sadhasivam, Hemavathy Nagarajan & Vetrivel Umashankar
Pages: 3131-3143
Published online: 12 Aug 2019
AbstractforStructure-based drug target prioritisation and rational drug design for targeting Chlamydia trachomatis eye infections | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 293 Views
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Article
Structural dynamics studies on the binding of aflatoxin B1 to chicken egg albumin using spectroscopic techniques and molecular docking
Mohd Aamir Qureshi & Saleem Javed
Pages: 3144-3155
Published online: 13 Aug 2019
AbstractforStructural dynamics studies on the binding of aflatoxin B1 to chicken egg albumin using spectroscopic techniques and molecular docking | Full Text | References | PDF (2.6 MB) | EPUB
  • 383 Views
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Article
Design, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes
Jingwei Wu, Yingzhan Sun, Hui Zhou, Ying Ma & Runling Wang
Pages: 3156-3165
Published online: 22 Aug 2019
AbstractforDesign, synthesis, biological evaluation and molecular dynamics simulation studies of (R)-5-methylthiazolidin-4-One derivatives as megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) inhibitors for the treatment of type 2 diabetes | Full Text | References | PDF (2.7 MB) | EPUB
  • 218 Views
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Article
Structure-based design of selective histone deacetylase 6 zinc binding groups
Leandro A. Alves Avelar, Dusan Ruzic, Nemanja Djokovic, Thomas Kurz & Katarina Nikolic
Pages: 3166-3177
Published online: 14 Aug 2019
AbstractforStructure-based design of selective histone deacetylase 6 zinc binding groups | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 334 Views
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Article
Binding properties of sodium glucose co-transporter-2 inhibitor empagliflozin to human serum albumin: spectroscopic methods and computer simulations
Wenjing Wang, Na Gan, Qiaomei Sun, Di Wu, Ludan Zhao, Zili Suo, Peixiao Tang & Hui Li
Pages: 3178-3187
Published online: 13 Aug 2019
AbstractforBinding properties of sodium glucose co-transporter-2 inhibitor empagliflozin to human serum albumin: spectroscopic methods and computer simulations | Full Text | References | PDF (2.3 MB) | EPUB
  • 230 Views
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Article
Neighboring base sequence effect on DNA damage
Young-Ae Lee, Ha Young Cho & Seog K. Kim
Pages: 3188-3195
Published online: 28 Aug 2019
AbstractforNeighboring base sequence effect on DNA damage | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 107 Views
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Article
Insights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations
Budheswar Dehury, Ning Tang & Kasper P. Kepp
Pages: 3196-3210
Published online: 09 Sep 2019
AbstractforInsights into membrane-bound presenilin 2 from all-atom molecular dynamics simulations | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 365 Views
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Article
In silico study revealed major conserve architectures and novel features of pyrabactin binding to Oryza sativa ABA receptors compare to the Arabidopsis thaliana
Manish K. Gupta, Vishakha Sharma, Sangram K. Lenka & Viswanathan Chinnusamy
Pages: 3211-3224
Published online: 09 Sep 2019
AbstractforIn silico study revealed major conserve architectures and novel features of pyrabactin binding to Oryza sativa ABA receptors compare to the Arabidopsis thaliana | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 228 Views
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Article
Potential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach
Georcki Ropón-Palacios, Manuel E. Chenet-Zuta, Gustavo E. Olivos-Ramirez, Kewin Otazu, Jorge Acurio-Saavedra & Ihosvany Camps
Pages: 3225-3234
Published online: 22 Aug 2019
AbstractforPotential novel inhibitors against emerging zoonotic pathogen Nipah virus: a virtual screening and molecular dynamics approach | Full Text | References | PDF (2.1 MB) | EPUB
  • 347 Views
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Article
Molecular docking and dynamics studies on novel benzene sulfonamide substituted pyrazole-pyrazoline analogues as potent inhibitors of Plasmodium falciparum Histo aspartic protease
Mahalakshmi Thillainayagam, Sudha Ramaiah & Anand Anbarasu
Pages: 3235-3245
Published online: 24 Aug 2019
AbstractforMolecular docking and dynamics studies on novel benzene sulfonamide substituted pyrazole-pyrazoline analogues as potent inhibitors of Plasmodium falciparum Histo aspartic protease | Full Text | References | PDF (2.2 MB) | EPUB
  • 291 Views
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Article
Synthesis, characterization, and anticancer activity of Schiff bases
Noor Uddin, Faisal Rashid, Saqib Ali, Syed Ahmed Tirmizi, Iqbal Ahmad, Sumera Zaib, Muhammad Zubair, Paula L. Diaconescu, Muhammad Nawaz Tahir, Jamshed Iqbal & Ali Haider
Pages: 3246-3259
Published online: 28 Aug 2019
AbstractforSynthesis, characterization, and anticancer activity of Schiff bases | Full Text | References | PDF (3.8 MB) | EPUB
  • 1443 Views
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Article
Small protein–protein interfaces rich in electrostatic are often linked to regulatory function
Christina Nilofer, Anshul Sukhwal, Arumugam Mohanapriya, Meena Kishore Sakharkar & Pandjassarame Kangueane
Pages: 3260-3279
Published online: 09 Sep 2019
AbstractforSmall protein–protein interfaces rich in electrostatic are often linked to regulatory function | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 177 Views
  • 3 CrossRef citations
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Article
Identification of potential histone deacetylase1 (HDAC1) inhibitors using multistep virtual screening approach including SVM model, pharmacophore modeling, molecular docking and biological evaluation
Shagun Krishna, Amar Deep Lakra, Nidhi Shukla, Saman Khan, Durga Prasad Mishra, Shakil Ahmed & Mohammad Imran Siddiqi
Pages: 3280-3295
Published online: 09 Sep 2019
AbstractforIdentification of potential histone deacetylase1 (HDAC1) inhibitors using multistep virtual screening approach including SVM model, pharmacophore modeling, molecular docking and biological evaluation | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 487 Views
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Article
Nucleobase sequence based building up of reliable QSAR models with the index of ideality correlation using Monte Carlo method
Parvin Kumar & Ashwani Kumar
Pages: 3296-3306
Published online: 09 Sep 2019
AbstractforNucleobase sequence based building up of reliable QSAR models with the index of ideality correlation using Monte Carlo method | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 302 Views
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Article
Design of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations
Takuya Ezawa, Satoshi Sugiyama, Ayami Ara, Ingebrigt Sylte & Noriyuki Kurita
Pages: 3307-3317
Published online: 29 Aug 2019
AbstractforDesign of galardine analogs as putative psudolysin inhibitors based on ab initio fragment molecular orbital calculations | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 119 Views
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Article
Another step toward understanding the binding mode of other derivatives of [Ru(phen)2L] complexes
Maryam Nejat Dehkordi & Per Lincoln
Pages: 3318-3326
Published online: 16 Oct 2019
AbstractforAnother step toward understanding the binding mode of other derivatives of [Ru(phen)2L] complexes | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 135 Views
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Article
New strategy for identifying potential natural HIV-1 non-nucleoside reverse transcriptase inhibitors against drug-resistance: an in silico study
Yanjing Wang, Xiangeng Wang, Yi Xiong, Aman Chandra Kaushik, Junaid Muhammad, Abbas Khan, Hao Dai & Dong-Qing Wei
Pages: 3327-3341
Published online: 03 Sep 2019
AbstractforNew strategy for identifying potential natural HIV-1 non-nucleoside reverse transcriptase inhibitors against drug-resistance: an in silico study | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 717 Views
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Article
Novel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays
Kader Sahin, Belma Zengin Kurt, Fatih Sonmez & Serdar Durdagi
Pages: 3342-3358
Published online: 06 Oct 2019
AbstractforNovel AChE and BChE inhibitors using combined virtual screening, text mining and in vitro binding assays | Full Text | References | PDF (5.6 MB) | EPUB
  • 521 Views
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Article
Deciphering the conformational preferences of furanosides. A molecular dynamics study
Karina Nester & Wojciech Plazinski
Pages: 3359-3370
Published online: 30 Aug 2019
AbstractforDeciphering the conformational preferences of furanosides. A molecular dynamics study | Full Text | References | PDF (2.7 MB) | EPUB
  • 198 Views
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Article
Effects of natural compounds on conformational properties and hairpin formation of amyloid-β42 monomer: docking and molecular dynamics simulation study
Mohammad Ghorbani, Hossein Soleymani, Abdollah Allahverdi, Seyedehsamaneh Shojaeilangari & Hossein Naderi-Manesh
Pages: 3371-3383
Published online: 15 Sep 2019
AbstractforEffects of natural compounds on conformational properties and hairpin formation of amyloid-β42 monomer: docking and molecular dynamics simulation study | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 203 Views
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Article
Design of dipicolinic acid derivatives as New Delhi metallo-β-lactamase-1 inhibitors using a combined computational approach
Xiyan Wang, Yawen Gao, Yiding Yu, Yanan Yang, Guizhen Wang, Lin Sun & Xiaodi Niu
Pages: 3384-3395
Published online: 24 Sep 2019
AbstractforDesign of dipicolinic acid derivatives as New Delhi metallo-β-lactamase-1 inhibitors using a combined computational approach | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 284 Views
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Article
Structure-based virtual screening, molecular dynamics simulation and MM-PBSA toward identifying the inhibitors for two-component regulatory system protein NarL of Mycobacterium Tuberculosis
Niranjan Kumar, Rakesh Srivastava, Amresh Prakash & Andrew. M. Lynn
Pages: 3396-3410
Published online: 26 Aug 2019
AbstractforStructure-based virtual screening, molecular dynamics simulation and MM-PBSA toward identifying the inhibitors for two-component regulatory system protein NarL of Mycobacterium Tuberculosis | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 1090 Views
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Article
Molecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation
Gaurava Srivastava, M. P. Darokar & Ashok Sharma
Pages: 3411-3431
Published online: 05 Sep 2019
AbstractforMolecular investigation against the resistant mechanism of PncA mutated pyrazinamide resistance and insight into the role of pH environment for pyrazinamide activation | Full Text | References | PDF (5.5 MB) | EPUB | Supplemental
  • 147 Views
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Letter to the Editor

Letter
Biodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis
Wafaa Hassan Muslem, Mohamed Faraj Edbeib, Hasan Murat Aksoy, Yilmaz Kaya, Azzmer Azzar Abdul Hamid, Mohammad Hakim Mohammad Hood, Roswanira Abdul Wahab & Fahrul Huyop
Pages: 3432-3441
Published online: 20 Aug 2019
First Page PreviewforBiodegradation of 3-chloropropionic acid (3-CP) by Bacillus cereus WH2 and its in silico enzyme-substrate docking analysis | Full Text | References | PDF (2.7 MB) | EPUB
  • 358 Views
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