Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 5 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 5 (2023)

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Vol 42, 2024 Volume 41, 2023 Vol 40, 2022 Vol 39, 2021 Vol 38, 2020 Vol 37, 2019 Vol 36, 2018 Vol 35, 2017 Vol 34, 2016 Vol 33, 2015 Vol 32, 2014 Vol 31, 2013 Vol 30, 2012 Vol 29, 2011-2012 Vol 28, 2010-2011 Vol 27, 2009-2010 Vol 26, 2008-2009 Vol 25, 2007-2008 Vol 24, 2006-2007 Vol 23, 2005-2006 Vol 22, 2004-2005 Vol 21, 2003-2004 Vol 20, 2002-2003 Vol 19, 2001-2002 Vol 18, 2000-2001 Vol 17, 1999-2000 Vol 16, 1998-1999 Vol 15, 1997-1998 Vol 14, 1996-1997 Vol 13, 1995-1996 Vol 12, 1994-1995 Vol 11, 1993-1994 Vol 10, 1992-1993 Vol 9, 1991-1992 Vol 8, 1990-1991 Vol 7, 1989-1990 Vol 6, 1988-1989 Vol 5, 1987-1988 Vol 4, 1986-1987 Vol 3, 1985-1986 Vol 2, 1984-1985 Vol 1, 1983-1984
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Research Articles

Article
Predictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2
Manoj Kumar Yadav, Shaban Ahmad, Khalid Raza, Sunil Kumar, Murugesh Eswaran & Mussuvir Pasha KM
Pages: 1527-1539
Published online: 03 Jan 2022
AbstractforPredictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2 | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
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Article
In silico screening-based discovery of inhibitors against glycosylation proteins dysregulated in cancer
Michael Russelle S. Alvarez, Sheryl Joyce B. Grijaldo, Ruel C. Nacario, Jomar F. Rabajante, Francisco M. Heralde III, Carlito B. Lebrilla & Gladys C. Completo
Pages: 1540-1552
Published online: 06 Jan 2022
AbstractforIn silico screening-based discovery of inhibitors against glycosylation proteins dysregulated in cancer | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 694 Views
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Article
Computer-based identification of olive oil components as a potential inhibitor of neirisaral adhesion a regulatory protein
Riyadh Ahmed Atto Al-Shuaeeb, A. A. Yassin, Mahmoud A. A. Ibrahim, H. R. Abd El-Mageed, M. A. Ghandour & M. M. Khalil
Pages: 1553-1560
Published online: 03 Jan 2022
AbstractforComputer-based identification of olive oil components as a potential inhibitor of neirisaral adhesion a regulatory protein | Full Text | References | PDF (1.2 MB) | EPUB
  • 320 Views
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Article
Coumarin derivative as a potent drug candidate against triple negative breast cancer targeting the frizzled receptor of wingless-related integration site signaling pathway
Akshay Uttarkar, Alice Preethi Kishore, Sudhanva M. Srinivas, Shobith Rangappa, Raviraj Kusanur & Vidya Niranjan
Pages: 1561-1573
Published online: 05 Jan 2022
AbstractforCoumarin derivative as a potent drug candidate against triple negative breast cancer targeting the frizzled receptor of wingless-related integration site signaling pathway | Full Text | References | PDF (3.3 MB) | EPUB
  • 621 Views
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Article
In silico bioprospecting of antiviral compounds from marine fungi and mushroom for rapid development of nutraceuticals against SARS-CoV-2
Amit Kumar Srivastav, Jyoti Jaiswal & Umesh Kumar
Pages: 1574-1585
Published online: 31 Dec 2021
AbstractforIn silico bioprospecting of antiviral compounds from marine fungi and mushroom for rapid development of nutraceuticals against SARS-CoV-2 | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 279 Views
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Article
The interaction of DNMT1 and DNMT3A epigenetic enzymes with phthalates and perfluoroalkyl substances: an in silico approach
Giorgia Innamorati, Maria Pierdomenico, Barbara Benassi & Caterina Arcangeli
Pages: 1586-1602
Published online: 06 Jan 2022
AbstractforThe interaction of DNMT1 and DNMT3A epigenetic enzymes with phthalates and perfluoroalkyl substances: an in silico approach | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 342 Views
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Article
Traditional herbal compounds as candidates to inhibit the SARS-CoV-2 main protease: an in silico study
Osmair Vital de Oliveira, Maria Cristina Andreazza Costa, Ricardo Marques da Costa, Rafael Giordano Viegas, Andrew S. Paluch & Márcia Miguel Castro Ferreira
Pages: 1603-1616
Published online: 04 Jan 2022
AbstractforTraditional herbal compounds as candidates to inhibit the SARS-CoV-2 main protease: an in silico study | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 352 Views
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Article
Modeling mRNA-based vaccine YFV.E1988 against yellow fever virus E-protein using immuno-informatics and reverse vaccinology approach
Nabiha Tasneem Khan, Maliha Afroj Zinnia & Abul Bashar Mir Md. Khademul Islam
Pages: 1617-1638
Published online: 07 Jan 2022
AbstractforModeling mRNA-based vaccine YFV.E1988 against yellow fever virus E-protein using immuno-informatics and reverse vaccinology approach | Full Text | References | PDF (6 MB) | EPUB | Supplemental
  • 620 Views
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Article
Ligand pathways in estrogen-related receptors
André Fischer, Ferhat Bardakci, Manuel Sellner, Markus A. Lill & Martin Smieško
Pages: 1639-1648
Published online: 24 Jan 2022
AbstractforLigand pathways in estrogen-related receptors | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 329 Views
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Article
Synthesis, in vitro biological screening and docking study of benzo[d]oxazole bis Schiff base derivatives as a potent anti-Alzheimer agent
Muhammad Taha, Fazal Rahim, Khalid Zaman, El Hassane Anouar, Nizam Uddin, Faisal Nawaz, Muhammad Sajid, Khalid Mohammed Khan, Adnan Ali Shah, Abdul Wadood, Ashfaq Ur Rehman & Amani H. Alhibshi
Pages: 1649-1664
Published online: 06 Jan 2022
AbstractforSynthesis, in vitro biological screening and docking study of benzo[d]oxazole bis Schiff base derivatives as a potent anti-Alzheimer agent | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 469 Views
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Article
Molecular dynamics simulations and in vitro studies of hybrid decellularized leaf-peptide-polypyrrole composites for potential tissue engineering applications
Saige M. Mitchell, Harrison T. Pajovich, Sarah M. Broas, Mindy M. Hugo & Ipsita A. Banerjee
Pages: 1665-1680
Published online: 06 Jan 2022
AbstractforMolecular dynamics simulations and in vitro studies of hybrid decellularized leaf-peptide-polypyrrole composites for potential tissue engineering applications | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 304 Views
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Article
Search for potentially biased epidermal growth factor receptor (EGFR) inhibitors through pharmacophore modelling, molecular docking, and molecular dynamics (MD) simulation approaches
Megha Jethwa, Aditi Gangopadhyay & Achintya Saha
Pages: 1681-1689
Published online: 11 Jan 2022
AbstractforSearch for potentially biased epidermal growth factor receptor (EGFR) inhibitors through pharmacophore modelling, molecular docking, and molecular dynamics (MD) simulation approaches | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 301 Views
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Article
Structural exploration of common pharmacophore based berberine derivatives as novel histone deacetylase inhibitor targeting HDACs enzymes
Saravanan Kandasamy, Manikandan Selvaraj, Karthikeyan Muthusamy, Naveena Varadaraju, Srinivasan Kannupal, Ashok Kumar Sekar & Ravikumar Vilwanathan
Pages: 1690-1703
Published online: 07 Jan 2022
AbstractforStructural exploration of common pharmacophore based berberine derivatives as novel histone deacetylase inhibitor targeting HDACs enzymes | Full Text | References | PDF (3.9 MB) | EPUB
  • 324 Views
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Article
Berberine chloride (dual topoisomerase I and II inhibitor) modulate mitochondrial uncoupling protein (UCP1) in molecular docking and dynamic with in-vitro cytotoxic and mitochondrial ATP production
Md. Reyad-ul Ferdous, Mohnad Abdalla, Mengjiao Yang, Li Xiaoling & Yongfeng Song
Pages: 1704-1714
Published online: 25 May 2022
AbstractforBerberine chloride (dual topoisomerase I and II inhibitor) modulate mitochondrial uncoupling protein (UCP1) in molecular docking and dynamic with in-vitro cytotoxic and mitochondrial ATP production | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 332 Views
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Article
An in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme
Ana Paula Lima da Costa, Fábio José Bonfim Cardoso & Fábio Alberto de Molfetta
Pages: 1715-1729
Published online: 07 Jan 2022
AbstractforAn in silico molecular modeling approach of halolactone derivatives as potential inhibitors for human immunodeficiency virus type-1 reverse transcriptase enzyme | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 180 Views
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Article
Antiproliferative studies of transition metal chelates of a pyrazolone based hydrazone derivative
Surya Philip, Elambalassery G. Jayasree & Kochukittan Mohanan
Pages: 1730-1744
Published online: 13 Jan 2022
AbstractforAntiproliferative studies of transition metal chelates of a pyrazolone based hydrazone derivative | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 175 Views
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Article
Charge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy
Suman Hait, Sudipto Basu & Sudip Kundu
Pages: 1745-1752
Published online: 07 Jan 2022
AbstractforCharge reversal mutations in mesophilic-thermophilic orthologous protein pairs and their role in enhancing coulombic interaction energy | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 140 Views
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Article
Synthesis, spectroscopic characterization, molecular docking and in vitro cytotoxicity investigations on 8-Amino-6-Methoxy Quinolinium Picrate: a novel breast cancer drug
R. Geetha, M. R. Meera, C. Vijayakumar, R. Premkumar & A. Milton Franklin Benial
Pages: 1753-1766
Published online: 05 Jan 2022
AbstractforSynthesis, spectroscopic characterization, molecular docking and in vitro cytotoxicity investigations on 8-Amino-6-Methoxy Quinolinium Picrate: a novel breast cancer drug | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 207 Views
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Article
Identification of SARS-CoV-2 main protease inhibitors from FDA-approved drugs by artificial intelligence-supported activity prediction system
Hirotsugu Komatsu, Takeshi Tanaka, Zhengmao Ye, Ken Ikeda, Takao Matsuzaki, Mayo Yasugi & Masato Hosoda
Pages: 1767-1775
Published online: 05 Jan 2022
AbstractforIdentification of SARS-CoV-2 main protease inhibitors from FDA-approved drugs by artificial intelligence-supported activity prediction system | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 315 Views
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Article
Computational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein
Omotayo O. Oyedara, Olatomide A. Fadare, Eduardo Franco-Frías, Norma Heredia & Santos García
Pages: 1776-1789
Published online: 07 Jan 2022
AbstractforComputational assessment of phytochemicals of medicinal plants from Mexico as potential inhibitors of Salmonella enterica efflux pump AcrB protein | Full Text | References | PDF (2.6 MB) | EPUB
  • 342 Views
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Article
QPoweredCompound2DeNovoDrugPropMax – a novel programmatic tool incorporating deep learning and in silico methods for automated in silico bio-activity discovery for any compound of interest
Ben Geoffrey A. S.Rafal Madaj & Pavan Preetham Valluri
Pages: 1790-1797
Published online: 10 Jan 2022
AbstractforQPoweredCompound2DeNovoDrugPropMax – a novel programmatic tool incorporating deep learning and in silico methods for automated in silico bio-activity discovery for any compound of interest | Full Text | References | PDF (1.4 MB) | EPUB
  • 257 Views
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Article
A benzimidazole scaffold as a promising inhibitor against SARS-CoV-2
Prafullya Kumar Mudi, Ayan Kumar Mahanty, Muddukrishnaiah Kotakonda, Sunnapu Prasad, Subires Bhattacharyya & Bhaskar Biswas
Pages: 1798-1810
Published online: 08 Jan 2022
AbstractforA benzimidazole scaffold as a promising inhibitor against SARS-CoV-2 | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 332 Views
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Article
Lead optimization, pharmacophore development and scaffold design of protein kinase CK2 inhibitors as potential COVID-19 therapeutics
Siddharth Yadav, Shahzaib Ahamad, Dinesh Gupta & Puniti Mathur
Pages: 1811-1827
Published online: 11 Jan 2022
AbstractforLead optimization, pharmacophore development and scaffold design of protein kinase CK2 inhibitors as potential COVID-19 therapeutics | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 444 Views
  • 1 CrossRef citations
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Article
Synthesis, characterizations of aryl-substituted dithiodibenzothioate derivatives, and investigating their anti-Alzheimer's properties
Ümit Çalışır, Yasemin Camadan, Baki Çiçek, Ebru Akkemik, Volkan Eyüpoğlu & Şevki Adem
Pages: 1828-1845
Published online: 12 Jan 2022
AbstractforSynthesis, characterizations of aryl-substituted dithiodibenzothioate derivatives, and investigating their anti-Alzheimer's properties | Full Text | References | PDF (4.7 MB) | EPUB | Supplemental
  • 428 Views
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Article
Molecular docking, molecular dynamics simulation and MM-GBSA studies of the activity of glycyrrhizin relevant substructures on SARS-CoV-2 RNA-dependent-RNA polymerase
Mazin A. Zamzami
Pages: 1846-1858
Published online: 17 Jan 2022
AbstractforMolecular docking, molecular dynamics simulation and MM-GBSA studies of the activity of glycyrrhizin relevant substructures on SARS-CoV-2 RNA-dependent-RNA polymerase | Full Text | References | PDF (3.3 MB) | EPUB
  • 338 Views
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Article
Immunoinformatics analysis for design of multi-epitope subunit vaccine by using heat shock proteins against Schistosoma mansoni
Nirali Pandya & Amit Kumar
Pages: 1859-1878
Published online: 18 Jan 2022
AbstractforImmunoinformatics analysis for design of multi-epitope subunit vaccine by using heat shock proteins against Schistosoma mansoni | Full Text | References | PDF (4.6 MB) | EPUB | Supplemental
  • 375 Views
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Article
On the recognition of Yersinia protein tyrosine phosphatase by carboxylic acid derivatives
Petar M. Mitrasinovic
Pages: 1879-1894
Published online: 12 Jan 2022
AbstractforOn the recognition of Yersinia protein tyrosine phosphatase by carboxylic acid derivatives | Full Text | References | PDF (2.6 MB) | EPUB
  • 116 Views
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Article
Bovine serum albumin interaction, molecular docking, anticancer and antimicrobial activities of Co(II) Schiff base complex derived from Nophen ligand
J. Jeevitha Rani, A. Mary Imelda Jayaseeli, M. Sankarganesh & R. Nandini Asha
Pages: 1895-1903
Published online: 17 Jan 2022
AbstractforBovine serum albumin interaction, molecular docking, anticancer and antimicrobial activities of Co(II) Schiff base complex derived from Nophen ligand | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 323 Views
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Article
N-acetylglucosamine-phosphatidylinositol de-N-acetylase as a novel target for probing potential inhibitor against Leishmania donovani
Mukesh Kumar, Manish Kumar Tripathi, Deepali Gupta, Sanjit Kumar, Nihar Ranjan Biswas, A. S. Ethayathulla & Punit Kaur
Pages: 1904-1918
Published online: 11 Jan 2022
AbstractforN-acetylglucosamine-phosphatidylinositol de-N-acetylase as a novel target for probing potential inhibitor against Leishmania donovani | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 210 Views
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Article
An investigation for the interaction of gamma oryzanol with the Mpro of SARS-CoV-2 to combat COVID-19: DFT, molecular docking, ADME and molecular dynamics simulations
Anirudh Pratap Singh Raman, Madhur Babu Singh, Vijay Kumar Vishvakarma, Pallavi Jain, Ajay Kumar, Shallu Sachdeva, Kamlesh Kumari & Prashant Singh
Pages: 1919-1929
Published online: 22 Jan 2022
AbstractforAn investigation for the interaction of gamma oryzanol with the Mpro of SARS-CoV-2 to combat COVID-19: DFT, molecular docking, ADME and molecular dynamics simulations | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 516 Views
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Article
Cytotoxic and apoptotic effects of some (R)-carvone-isoxazoline derivatives on human fibrosarcoma and carcinoma cells: experimental evaluation for cytotoxicity, molecular docking and molecular dynamics studies
Ali Oubella, Abdoullah Bimoussa, Said Byadi, Yassine Laamari, Mourad Fawzi, Abdellah N’ait ousidi, Domen Oblak, Aziz Auhmani, Abdelkhalek Riahi, Hamid Morjani & My Youssef Ait Itto
Pages: 1930-1943
Published online: 11 Jan 2022
AbstractforCytotoxic and apoptotic effects of some (R)-carvone-isoxazoline derivatives on human fibrosarcoma and carcinoma cells: experimental evaluation for cytotoxicity, molecular docking and molecular dynamics studies | Full Text | References | PDF (3.2 MB) | EPUB
  • 234 Views
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Article
Design, synthesis, molecular modeling, DFT, ADME and biological evaluation studies of some new 1,3,4-oxadiazole linked benzimidazoles as anticancer agents and aromatase inhibitors
Ulviye Acar Çevik, Ismail Celik, Ayşen Işık, Iqrar Ahmad, Harun Patel, Yusuf Özkay & Zafer Asım Kaplancıklı
Pages: 1944-1958
Published online: 17 Jan 2022
AbstractforDesign, synthesis, molecular modeling, DFT, ADME and biological evaluation studies of some new 1,3,4-oxadiazole linked benzimidazoles as anticancer agents and aromatase inhibitors | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 1151 Views
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Article
Molecular modelling and structure-activity relationship of a natural derivative of o-hydroxybenzoate as a potent inhibitor of dual NSP3 and NSP12 of SARS-CoV-2: in silico study
Yusuf Oloruntoyin Ayipo, Iqrar Ahmad, Yahaya Sani Najib, Sikirat Kehinde Sheu, Harun Patel & Mohd Nizam Mordi
Pages: 1959-1977
Published online: 17 Jan 2022
AbstractforMolecular modelling and structure-activity relationship of a natural derivative of o-hydroxybenzoate as a potent inhibitor of dual NSP3 and NSP12 of SARS-CoV-2: in silico study | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 484 Views
  • 11 CrossRef citations
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Article
In silico identification of potential phytochemical inhibitors targeting farnesyl diphosphate synthase of cotton bollworm (Helicoverpa armigera)
Md Shahid Alam, Monica Sharma, Rakesh Kumar, Joy Das, Surabhi Rode, Pravindra Kumar, Ramasare Prasad & Ashwani Kumar Sharma
Pages: 1978-1987
Published online: 17 Jan 2022
AbstractforIn silico identification of potential phytochemical inhibitors targeting farnesyl diphosphate synthase of cotton bollworm (Helicoverpa armigera) | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 987 Views
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Article
Discovery of new 1,4-disubstituted 1,2,3-triazoles: in silico ADME profiling, molecular docking and biological evaluation studies
İrfan Şahin, Mustafa Çeşme, Neslihan Yüce & Ferhan Tümer
Pages: 1988-2001
Published online: 20 Jan 2022
AbstractforDiscovery of new 1,4-disubstituted 1,2,3-triazoles: in silico ADME profiling, molecular docking and biological evaluation studies | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 547 Views
  • 8 CrossRef citations
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Article
Identification of natural products against enoyl-acyl-carrier-protein reductase in malaria via combined pharmacophore modeling, molecular docking and simulations studies
Anu Manhas, Amar Ghosh, Yogesh Verma, Tanay Das & Prakash C. Jha
Pages: 2002-2015
Published online: 19 Jan 2022
AbstractforIdentification of natural products against enoyl-acyl-carrier-protein reductase in malaria via combined pharmacophore modeling, molecular docking and simulations studies | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 251 Views
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Article
Descriptor-free QSAR: effectiveness in screening for putative inhibitors of FGFR1
I. Y. Joel, L. A. Sulaimon, M. O. Idris, T. O. Adigun, R. A. Adisa, T. A. Ademoye, M. O. Ogunleye & T. O. Olaniyi
Pages: 2016-2032
Published online: 25 Jan 2022
AbstractforDescriptor-free QSAR: effectiveness in screening for putative inhibitors of FGFR1 | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 285 Views
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Article
Virtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease
Aakriti Garg, Narender Goel, Nipun Abhinav, Tanmay Varma, Anushree Achari, Pinaki Bhattacharjee, Izaz Monir Kamal, Saikat Chakrabarti, Velayutham Ravichandiran, Araveeti Madhusudhana Reddy, Sreya Gupta & Parasuraman Jaisankar
Pages: 2033-2045
Published online: 19 Jan 2022
AbstractforVirtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 539 Views
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Review Article

Review Article
Detailed investigation of catalytically important residues of class A β-lactamase
Vidhu Agarwal, Tara Chand Yadav, Akhilesh Tiwari & Pritish Varadwaj
Pages: 2046-2073
Published online: 06 Jan 2022
AbstractforDetailed investigation of catalytically important residues of class A β-lactamase | Full Text | References | PDF (3.4 MB) | EPUB
  • 259 Views
  • 1 CrossRef citations
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