Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 16 (2022)

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Journal of Biomolecular Structure and Dynamics, Volume 40, Issue 16 (2022)

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Research Articles

Article
Bioinformatics analysis of extracellular subtilisin E from Bacillus subtilis
Reza Zolfaghari Emameh, Justina Kazokaitė & Bagher Yakhchali
Pages: 7183-7190
Published online: 04 Mar 2021
AbstractforBioinformatics analysis of extracellular subtilisin E from Bacillus subtilis | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 376 Views
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Article
Evolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress
Sameer Hassan, Katrin Berk & Henrik Aronsson
Pages: 7191-7204
Published online: 23 Mar 2021
AbstractforEvolution and identification of DREB transcription factors in the wheat genome: modeling, docking and simulation of DREB proteins associated with salt stress | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 2729 Views
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Open Access
Article
Newly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies
Mouhi Eddine Hachim, Ali Oubella, Said Byadi, Mourad Fawzi, Yassine Laamari, Lahoucine Bahsis, Aziz Aboulmouhajir, Hamid Morjani, Črtomir Podlipnik, Aziz Auhmani & My Youssef Ait Itto
Pages: 7205-7217
Published online: 15 Mar 2021
AbstractforNewly synthesized (R)-carvone-derived 1,2,3-triazoles: structural, mechanistic, cytotoxic and molecular docking studies | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 344 Views
  • 10 CrossRef citations
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Article
A comprehensive in silico and in vitro studies on quinizarin: a promising phytochemical derived from Rhizophora mucronata Lam
V. Sachithanandam, P. Lalitha, A. Parthiban, Jayaraman Muthukumaran, Monika Jain, Ranjita Misra, T. Mageswaran, R. Sridhar, R. Purvaja & R. Ramesh
Pages: 7218-7229
Published online: 08 Mar 2021
AbstractforA comprehensive in silico and in vitro studies on quinizarin: a promising phytochemical derived from Rhizophora mucronata Lam | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 266 Views
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Article
Structural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2
Shruti Koulgi, Vinod Jani, Mallikarjunachari Uppuladinne V N, Uddhavesh Sonavane & Rajendra Joshi
Pages: 7230-7244
Published online: 08 Mar 2021
AbstractforStructural insight into the binding interactions of NTPs and nucleotide analogues to RNA dependent RNA polymerase of SARS-CoV-2 | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 276 Views
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Article
Alkaloids of Adhatoda vasica Nees. as potential inhibitors of cyclooxygenases – an in-silico study
Prasanth Ghanta, Mukesh Doble & Basavaraju Ramaiah
Pages: 7245-7255
Published online: 10 Mar 2021
AbstractforAlkaloids of Adhatoda vasica Nees. as potential inhibitors of cyclooxygenases – an in-silico study | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 248 Views
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Article
Implementation of computational approaches to explore the deleterious effects of non-synonymous SNPs on pRB protein
Md. Mashiur Rahaman, Rahatul Islam, G. M. Nurnabi Azad Jewel & Hammadul Hoque
Pages: 7256-7273
Published online: 08 Mar 2021
AbstractforImplementation of computational approaches to explore the deleterious effects of non-synonymous SNPs on pRB protein | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 254 Views
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Article
Fine-tuning pharmacological properties of mirtazapine antidepressant drug: a theoretical study
Yu Yang, Zhao Guangrong, Wang Xiaojing & Wei Gu
Pages: 7274-7282
Published online: 09 Mar 2021
AbstractforFine-tuning pharmacological properties of mirtazapine antidepressant drug: a theoretical study | Full Text | References | PDF (2.3 MB) | EPUB
  • 130 Views
  • 1 CrossRef citations
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Article
Immunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria
Ohilebo Abdulateef Abass, Vladimir I. Timofeev, Bishajit Sarkar, Desmond Odiamehi Onobun, Samuel Olarewaju Ogunsola, Ademola Emmanuel Aiyenuro, Abdullahi Tunde Aborode, Adebayo Emmanuel Aigboje, Basheer Nabilat Omobolanle, Anthony Goodwill Imolele & Alade Adebowale Abiodun
Pages: 7283-7302
Published online: 15 Mar 2021
AbstractforImmunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 265 Views
  • 3 CrossRef citations
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Article
Binding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV‐2: a molecular docking, molecular dynamics and MM/PBSA approach
Krishnendu Bera
Pages: 7303-7310
Published online: 08 Mar 2021
AbstractforBinding and inhibitory effect of ravidasvir on 3CLpro of SARS-CoV‐2: a molecular docking, molecular dynamics and MM/PBSA approach | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 427 Views
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Article
Potential inhibitors of angiotensin converting enzyme 2 receptor of COVID-19 by Corchorus olitorius Linn using docking, molecular dynamics, conceptual DFT investigation and pharmacophore mapping
Fouzia Mesli, Meriem Ghalem, Ismail Daoud & Said Ghalem
Pages: 7311-7323
Published online: 11 Mar 2021
AbstractforPotential inhibitors of angiotensin converting enzyme 2 receptor of COVID-19 by Corchorus olitorius Linn using docking, molecular dynamics, conceptual DFT investigation and pharmacophore mapping | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 317 Views
  • 7 CrossRef citations
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Article
Insights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling
Eric A. Zizzi, Marco Cavaglià, Jack A. Tuszynski & Marco A. Deriu
Pages: 7324-7338
Published online: 10 Mar 2021
AbstractforInsights into the interaction dynamics between volatile anesthetics and tubulin through computational molecular modelling | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 258 Views
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Article
Anti-glycemic potential of benzophenone thio/semicarbazone derivatives: synthesis, enzyme inhibition and ligand docking studies
Arshia, Sharmeen Fayyaz, Muniza Shaikh, Khalid Mohammed Khan & M. Iqbal Choudhary
Pages: 7339-7350
Published online: 26 Mar 2021
AbstractforAnti-glycemic potential of benzophenone thio/semicarbazone derivatives: synthesis, enzyme inhibition and ligand docking studies | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 225 Views
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Article
Flavonoid content of the Libyan Onosma Cyrenaicum: isolation, identification, electronic chemical reactivity, drug likeness, docking, and MD study
Ghazala Elkwafi, Najwa Mohamed, Fakhri Elabbar & Radwan Alnajjar
Pages: 7351-7366
Published online: 09 Mar 2021
AbstractforFlavonoid content of the Libyan Onosma Cyrenaicum: isolation, identification, electronic chemical reactivity, drug likeness, docking, and MD study | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 202 Views
  • 1 CrossRef citations
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Article
Antiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection
Dennis C. Copertino Jr., Bruno C. Casado Lima, Rodrigo R. R. Duarte, Timothy R. Powell, Christopher E. Ormsby, Timothy Wilkin, Roy M. Gulick, Miguel de Mulder Rougvie & Douglas F. Nixon
Pages: 7367-7380
Published online: 18 Mar 2021
AbstractforAntiretroviral drug activity and potential for pre-exposure prophylaxis against COVID-19 and HIV infection | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 2947 Views
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Open Access
Article
Deciphering the effect of hydrophobicity on protein binding interaction in cobalt(II) complexes by multispectroscopic and computational methods
Masrat Bashir, Imtiyaz Yousuf, Farukh Arjmand & Sartaj Tabassum
Pages: 7381-7393
Published online: 09 Mar 2021
AbstractforDeciphering the effect of hydrophobicity on protein binding interaction in cobalt(II) complexes by multispectroscopic and computational methods | Full Text | References | PDF (4.2 MB) | EPUB | Supplemental
  • 83 Views
  • 3 CrossRef citations
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Article
Insilico drug designing for COVID-19: an approach of high-throughput virtual screening, molecular, and essential dynamics simulations
Rakesh Kumar, Rahul Kumar & Pranay Tanwar
Pages: 7394-7407
Published online: 10 Mar 2021
AbstractforInsilico drug designing for COVID-19: an approach of high-throughput virtual screening, molecular, and essential dynamics simulations | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 232 Views
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Article
An in-silico approach to identify the potential hot spots in SARS-CoV-2 spike RBD to block the interaction with ACE2 receptor
Antony Stalin, Ding Lin, Balakrishnan Senthamarai Kannan, Yue Feng, Yanjing Wang, Wei Zhao, Savarimuthu Ignacimuthu, Dong-Qing Wei & Yuan Chen
Pages: 7408-7423
Published online: 09 Mar 2021
AbstractforAn in-silico approach to identify the potential hot spots in SARS-CoV-2 spike RBD to block the interaction with ACE2 receptor | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 472 Views
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Article
N-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking studies
Seyit Ali Güngör, Mehmet Tümer, Muhammet Köse & Sultan Erkan
Pages: 7424-7438
Published online: 11 Mar 2021
AbstractforN-substituted benzenesulfonamide compounds: DNA binding properties and molecular docking studies | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 613 Views
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Article
Active site dynamics and catalytic mechanism in arabinan hydrolysis catalyzed by GH43 endo-arabinanase from QM/MM molecular dynamics simulation and potential energy surface
Wijitra Meelua, Tanchanok Wanjai, Natechanok Thinkumrob, Julianna Oláh, Jon I. Mujika, James R. Ketudat-Cairns, Supa Hannongbua & Jitrayut Jitonnom
Pages: 7439-7449
Published online: 10 Mar 2021
AbstractforActive site dynamics and catalytic mechanism in arabinan hydrolysis catalyzed by GH43 endo-arabinanase from QM/MM molecular dynamics simulation and potential energy surface | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 406 Views
  • 3 CrossRef citations
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Article
Structure-based design of small molecule and peptide inhibitors for selective targeting of ROCK1: an integrative computational approach
Samdani Ansar & Umashankar Vetrivel
Pages: 7450-7468
Published online: 10 Mar 2021
AbstractforStructure-based design of small molecule and peptide inhibitors for selective targeting of ROCK1: an integrative computational approach | Full Text | References | PDF (6 MB) | EPUB | Supplemental
  • 269 Views
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Article
Microsecond simulation analysis of carbonic anhydrase – II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity
Pulala Raghuveer Yadav, Syed Hussain Basha, Sadam D. V. Satyanarayana & Pavan Kumar Pindi
Pages: 7469-7482
Published online: 15 Mar 2021
AbstractforMicrosecond simulation analysis of carbonic anhydrase – II in complex with (+)-cathechin revealed molecular interactions responsible for its amelioration effect on fluoride toxicity | Full Text | References | PDF (4.6 MB) | EPUB
  • 167 Views
  • 2 CrossRef citations
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Article
Molecular and functional characterization of spotted snakehead NOD1 with an emphasis on structural insights into iE-DAP binding motifs employing advanced bioinformatic tools
Bhawna Chuphal, Umesh Rai, Rakesh Kumar & Brototi Roy
Pages: 7483-7495
Published online: 12 Mar 2021
AbstractforMolecular and functional characterization of spotted snakehead NOD1 with an emphasis on structural insights into iE-DAP binding motifs employing advanced bioinformatic tools | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 148 Views
  • 1 CrossRef citations
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Article
Pan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species
Andrei G. Felice, Leandro G. Alves, Alissa S. F. Freitas, Thaís C. V. Rodrigues, Arun K. Jaiswal, Sandeep Tiwari, Lucas G. R. Gomes, Fábio M. Miranda, Rommel T. J. Ramos, Vasco Azevedo, Letícia C. Oliveira, Carlo J. Oliveira, Siomar d. C. Soares & Leandro J. Benevides
Pages: 7496-7510
Published online: 15 Mar 2021
AbstractforPan-genomic analyses of 47 complete genomes of the Rickettsia genus and prediction of new vaccine targets and virulence factors of the species | Full Text | References | PDF (5.1 MB) | EPUB | Supplemental
  • 272 Views
  • 1 CrossRef citations
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Article
Target2DeNovoDrug: a novel programmatic tool for in silico-deep learning based de novo drug design for any target of interest
Rafal Madaj, Ben Geoffrey, Akhil Sanker & Pavan Preetham Valluri
Pages: 7511-7516
Published online: 11 Mar 2021
AbstractforTarget2DeNovoDrug: a novel programmatic tool for in silico-deep learning based de novo drug design for any target of interest | Full Text | References | PDF (1.7 MB) | EPUB
  • 421 Views
  • 3 CrossRef citations
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Article
Potentiality of Moringa oleifera against SARS-CoV-2: identified by a rational computer aided drug design method
Debanjan Sen, Samhita Bhaumik, Pradip Debnath & Sudhan Debnath
Pages: 7517-7534
Published online: 15 Mar 2021
AbstractforPotentiality of Moringa oleifera against SARS-CoV-2: identified by a rational computer aided drug design method | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 508 Views
  • 13 CrossRef citations
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Article
Unraveling the potential role of bioactive molecules produced by Trichoderma spp. as inhibitors of tomatinase enzyme having an important role in wilting disease: an in-silico approach
Garima Singh, Abhay Tiwari, Gourav Choudhir, Hariprasad P, Anuj Kumar & Satyawati Sharma
Pages: 7535-7544
Published online: 15 Mar 2021
AbstractforUnraveling the potential role of bioactive molecules produced by Trichoderma spp. as inhibitors of tomatinase enzyme having an important role in wilting disease: an in-silico approach | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 503 Views
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Article
Molecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis
Suresh Palanivel, Olli Yli-Harja & Meenakshisundaram Kandhavelu
Pages: 7545-7554
Published online: 22 Mar 2021
AbstractforMolecular interaction study of novel indoline derivatives with EGFR-kinase domain using multiple computational analysis | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 278 Views
  • 3 CrossRef citations
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Article
Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors
Alexander M. Andrianov, Grigory I. Nikolaev, Nikita A. Shuldov, Ivan P. Bosko, Arseny I. Anischenko & Alexander V. Tuzikov
Pages: 7555-7573
Published online: 15 Apr 2021
AbstractforApplication of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors | Full Text | References | PDF (3.3 MB) | EPUB
  • 645 Views
  • 8 CrossRef citations
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Article
Methoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays
Verônica M. Almeida, Êuder R. Dias, Bruno C. Souza, Jorddy N. Cruz, Cleydson B. R. Santos, Franco H. A. Leite, Raphael F. Queiroz & Alexsandro Branco
Pages: 7574-7583
Published online: 19 Mar 2021
AbstractforMethoxylated flavonols from Vellozia dasypus Seub ethyl acetate active myeloperoxidase extract: in vitro and in silico assays | Full Text | References | PDF (2.2 MB) | EPUB
  • 354 Views
  • 22 CrossRef citations
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Article
Ligand based 3D-QSAR model, pharmacophore, molecular docking and ADME to identify potential fibroblast growth factor receptor 1 inhibitors
Lu Huang, Xulong Wu, Xiaoli Fu, Haoxiang Wang, Biao Tang, Yirong Xiao, Caixia Zhou, Zhiqiao Zhao, Yujun Wan, Hui Chen, Zizhong Tang, Huipeng Yao, Zhi Shan & Tongliang Bu
Pages: 7584-7597
Published online: 18 Mar 2021
AbstractforLigand based 3D-QSAR model, pharmacophore, molecular docking and ADME to identify potential fibroblast growth factor receptor 1 inhibitors | Full Text | References | PDF (3.1 MB) | EPUB
  • 315 Views
  • 3 CrossRef citations
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Article
Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA
Mohd Mustafa, Asif Ali, Shahid Ali Siddiqui, Abdul Rouf Mir, Tasneem Kausar, Shahid M. Nayeem, Minhal Abidi & Safia Habib
Pages: 7598-7611
Published online: 15 Mar 2021
AbstractforBiophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA | Full Text | References | PDF (2.8 MB) | EPUB
  • 181 Views
  • 2 CrossRef citations
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Review Articles

Review Article
Pharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin
Duaa Ahmad Khan, Syed Damin Abbas Hamdani, Sahar Iftikhar, Sohaib Zafar Malik, Najam-us-Sahar Sadaf Zaidi, Alvina Gul, Mustafeez Mujtaba Babar, Munir Ozturk, Bengu Turkyilmaz Unal & Tuba Gonenc
Pages: 7612-7628
Published online: 04 Mar 2021
AbstractforPharmacoinformatics approaches in the discovery of drug-like antimicrobials of plant origin | Full Text | References | PDF (1.9 MB) | EPUB
  • 448 Views
  • 3 CrossRef citations
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Review Article
Cyanobacterial natural products as sources for antiviral drug discovery against COVID-19
Samaneh Jafari Porzani, Ozcan Konur & Bahareh Nowruzi
Pages: 7629-7644
Published online: 22 Mar 2021
AbstractforCyanobacterial natural products as sources for antiviral drug discovery against COVID-19 | Full Text | References | PDF (1.9 MB) | EPUB
  • 411 Views
  • 8 CrossRef citations
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