Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 1 (2024)

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Journal of Biomolecular Structure and Dynamics, Volume 42, Issue 1 (2024)

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Volume 42, 2024 Vol 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
Can de-phosphorylation of serine-5 in the C-terminal domain of human polymerase II affect its interaction with the PA C-terminal domain of bat Flu A polymerase?
Ahmed Samir, Wael Elshemey & Abdo Elfiky
Pages: 1-10
Published online: 01 Dec 2022
AbstractforCan de-phosphorylation of serine-5 in the C-terminal domain of human polymerase II affect its interaction with the PA C-terminal domain of bat Flu A polymerase? | Full Text | References | PDF (1.7 MB) | EPUB
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Article
Molecular screening reveals Variolin B as a multitargeted inhibitor of lung cancer: a molecular docking-based fingerprinting and molecular dynamics simulation study
Hassan H. Almasoudi, Mutaib M. Mashraqi, Saleh Alshamrani, Ohud Alsalmi, Afaf Awwadh Alharthi & Amal F. Gharib
Pages: 11-21
Published online: 28 Dec 2023
AbstractforMolecular screening reveals Variolin B as a multitargeted inhibitor of lung cancer: a molecular docking-based fingerprinting and molecular dynamics simulation study | Full Text | References | PDF (1.9 MB) | EPUB
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Article
Computational design of scFv anti-receptor binding domain of SARS-CoV-2 spike protein based on antibody S230 anti-SARS-CoV-1
Ade R. R. Firdaus, Umi Baroroh, Taufik Ramdani Tohari, Ari Hardianto, Toto Subroto & Muhammad Yusuf
Pages: 22-33
Published online: 28 Dec 2023
AbstractforComputational design of scFv anti-receptor binding domain of SARS-CoV-2 spike protein based on antibody S230 anti-SARS-CoV-1 | Full Text | References | PDF (2.4 MB) | EPUB
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Article
Investigation of Bucillamine as anti-COVID-19 drug: DFT study, molecular docking, molecular dynamic simulation and ADMET analysis
Fengwen Huang & Chen Chen
Pages: 34-42
Published online: 30 Mar 2023
AbstractforInvestigation of Bucillamine as anti-COVID-19 drug: DFT study, molecular docking, molecular dynamic simulation and ADMET analysis | Full Text | References | PDF (1.5 MB) | EPUB
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Article
Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods
Roy Dinata, Nisekhoto Nisa, Chettri Arati, Borgohain Rasmita, Chetia Uditraj, Rajkonwar Siddhartha, Baishya Bhanushree, Laskar Saeed-Ahmed, Bose Manikandan, Rema Momin Bidanchi, Giri Abinash, Buragohain Pori, Maurya Khushboo, Vikas Kumar Roy & Guruswami Gurusubramanian
Pages: 43-81
Published online: 05 Apr 2023
AbstractforRepurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods | Full Text | References | PDF (6.5 MB) | EPUB | Supplemental
  • 322 Views
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Article
Identifying novel therapeutic inhibitors to target FMS-like tyrosine kinase-3 (FLT3) against acute myeloid leukemia: a molecular docking, molecular dynamics, and DFT study
Md Rashedul Islam, Osman I. Osman & Walid M. I. Hassan
Pages: 82-100
Published online: 30 Mar 2023
AbstractforIdentifying novel therapeutic inhibitors to target FMS-like tyrosine kinase-3 (FLT3) against acute myeloid leukemia: a molecular docking, molecular dynamics, and DFT study | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
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Article
In silico modeling revealed phytomolecules derived from Cymbopogon citratus (DC.) leaf extract as promising candidates for malaria therapy
Ikponmwosa Owen Evbuomwan, Omokolade Oluwaseyi Alejolowo, Tobiloba Christiana Elebiyo, Charles Obiora Nwonuma, Oluwafemi Adeleke Ojo, Evelyn Uwa Edosomwan, Joy Ifeyinwa Chikwendu, Nwanneka Victoria Elosiuba, Justina Chimezie Akulue, Festus Ayorinde Dogunro, Damilare Emmanuel Rotimi, Omorefosa Osarenkhoe Osemwegie, Adebola Busola Ojo, Olusegun George Ademowo, Oluyomi Stephen Adeyemi & Olarewaju Michael Oluba
Pages: 101-118
Published online: 28 Mar 2023
AbstractforIn silico modeling revealed phytomolecules derived from Cymbopogon citratus (DC.) leaf extract as promising candidates for malaria therapy | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 211 Views
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Article
A combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives
Abdelmadjid Guendouzi, Lotfi Belkhiri, Abdelkrim Guendouzi, Tahar Mohamed Taha Derouiche & Abdelhamid Djekoun
Pages: 119-133
Published online: 30 Mar 2023
AbstractforA combined in silico approaches of 2D-QSAR, molecular docking, molecular dynamics and ADMET prediction of anti-cancer inhibitor activity for actinonin derivatives | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
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Article
New sulfa drug derivatives and their zinc(II) complexes: synthesis, spectroscopic properties and in vitro cytotoxic activities
Hakan Şahal, Samet Öz, Tuba Keskin, Suat Tekin, Erdal Canpolat & Mehmet Kaya
Pages: 134-147
Published online: 28 Mar 2023
AbstractforNew sulfa drug derivatives and their zinc(II) complexes: synthesis, spectroscopic properties and in vitro cytotoxic activities | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
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Article
2D-QSAR, molecular docking and MD simulation based virtual screening of the herbal molecules against Alzheimer’s disorder: an approach to predict CNS activity
Aman Thakur, Bhanu Sharma, Arun Parashar, Vivek Sharma, Ajay Kumar & Vineet Mehta
Pages: 148-162
Published online: 27 Mar 2023
Abstractfor2D-QSAR, molecular docking and MD simulation based virtual screening of the herbal molecules against Alzheimer’s disorder: an approach to predict CNS activity | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 272 Views
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Article
Antioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla
Mehmet Reşit Taysi, Muammer Kirici, Mahinur Kirici, Burak Tuzun & Alireza Poustforoosh
Pages: 163-176
Published online: 28 Mar 2023
AbstractforAntioxidant enzyme activities, molecular docking studies, MM-GBSA, and molecular dynamic of chlorpyrifos in freshwater fish Capoeta umbla | Full Text | References | PDF (2.4 MB) | EPUB
  • 343 Views
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Article
Identification of potential inhibitor against CTX-M-3 and CTX-M-15 proteins: an in silico and in vitro study
Bipasa Kar, Chanakya Nath Kundu, Mahender Kumar Singh, Budheswar Dehury, Sanghamitra Pati & Debdutta Bhattacharya
Pages: 177-193
Published online: 30 Mar 2023
AbstractforIdentification of potential inhibitor against CTX-M-3 and CTX-M-15 proteins: an in silico and in vitro study | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 270 Views
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Article
Large-scale computational screening of Indian medicinal plants reveals Cassia angustifolia to be a potentially anti-diabetic
Vinod Devaraji, Jayanthi Sivaraman & S. Prabhu
Pages: 194-210
Published online: 24 Mar 2023
AbstractforLarge-scale computational screening of Indian medicinal plants reveals Cassia angustifolia to be a potentially anti-diabetic | Full Text | References | PDF (2.7 MB) | EPUB
  • 243 Views
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Article
Synergistic antimicrobial activity, MD simulation studies and crystal structure of natural alcohol motif containing novel substituted cinnamates
Iram Irfan, Asghar Ali, Ayesha Ubaid, Yeshfeen Sherwani, Bhoomika Arora, Md. Musawwer Khan, Mukesh C. Joshi & Mohammad Abid
Pages: 211-230
Published online: 30 Mar 2023
AbstractforSynergistic antimicrobial activity, MD simulation studies and crystal structure of natural alcohol motif containing novel substituted cinnamates | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 163 Views
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Article
Electronic, mechanical, and thermal properties of zirconium dioxide nanotube interacting with poly lactic-co-glycolic acid and chitosan as potential agents in bone tissue engineering: insights from computational approaches
Atiah H. Almalki, Amany Belal, Ahmed A. Farghali, Rehab Mahmoud, F. M. Mustafa & H. R. Abd El-Mageed
Pages: 231-243
Published online: 30 Mar 2023
AbstractforElectronic, mechanical, and thermal properties of zirconium dioxide nanotube interacting with poly lactic-co-glycolic acid and chitosan as potential agents in bone tissue engineering: insights from computational approaches | Full Text | References | PDF (2.7 MB) | EPUB
  • 146 Views
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Article
Design and synthesis of 2-amino-4,6-diarylpyrimidine derivatives as potent α-glucosidase and α-amylase inhibitors: structure–activity relationship, in vitro, QSAR, molecular docking, MD simulations and drug-likeness studies
Ehsan Ullah Mughal, Samreen Amjid, Amina Sadiq, Nafeesa Naeem, Yasir Nazir, H. A. Alrafai, Abeer A. Hassan, Samar Y. Al-Nami, Amal A. Abdel Hafez, Syed Wadood Ali Shah & Mehreen Ghias
Pages: 244-260
Published online: 25 Apr 2023
AbstractforDesign and synthesis of 2-amino-4,6-diarylpyrimidine derivatives as potent α-glucosidase and α-amylase inhibitors: structure–activity relationship, in vitro, QSAR, molecular docking, MD simulations and drug-likeness studies | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 276 Views
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Article
Discovery of potent DNMT1 inhibitors against sickle cell disease using structural-based virtual screening, MM-GBSA and molecular dynamics simulation-based approaches
Chandu Ala, Renuka Parshuram Joshi, Pragya Gupta, Sivaprakash Ramalingam & Murugesan Sankaranarayanan
Pages: 261-273
Published online: 16 Apr 2023
AbstractforDiscovery of potent DNMT1 inhibitors against sickle cell disease using structural-based virtual screening, MM-GBSA and molecular dynamics simulation-based approaches | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 425 Views
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Article
Paradoxical effect of Aβ on protein levels of ABCA1 in astrocytes, microglia, and neurons isolated from C57BL/6 mice: an in vitro and in silico study to elucidate the effect of Aβ on ABCA1 in the brain cells
Vahid Zarezade, Zahra Nazeri, Shirin Azizidoost, Maryam Cheraghzadeh, Hossein Babaahmadi-Rezaei & Alireza Kheirollah
Pages: 274-287
Published online: 27 Apr 2023
AbstractforParadoxical effect of Aβ on protein levels of ABCA1 in astrocytes, microglia, and neurons isolated from C57BL/6 mice: an in vitro and in silico study to elucidate the effect of Aβ on ABCA1 in the brain cells | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 276 Views
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Article
Fragment-based design and MD simulations of human papilloma virus-16 E6 protein inhibitors
Vani Vemula, Amarnath Satheesh Marudamuthu, Sanjay Prasad, Suman B M, Mamatha S E, Swathi A, Priyanka Seal & Manikandan Alagumuthu
Pages: 288-297
Published online: 26 Apr 2023
AbstractforFragment-based design and MD simulations of human papilloma virus-16 E6 protein inhibitors | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 221 Views
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Article
Cheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy
Jamiu Olaseni Aribisala & Saheed Sabiu
Pages: 298-313
Published online: 28 Mar 2023
AbstractforCheminformatics identification of phenolics as modulators of penicillin-binding protein-3 of Pseudomonas aeruginosa towards interventive antibacterial therapy | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 301 Views
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Article
Inhibitory effect of acarbose on tyrosinase: application of molecular dynamics integrating inhibition kinetics
Jie-Hao Xu, Jinhyuk Lee, Shang-Jun Yin, Wei Wang & Yong-Doo Park
Pages: 314-325
Published online: 30 Mar 2023
AbstractforInhibitory effect of acarbose on tyrosinase: application of molecular dynamics integrating inhibition kinetics | Full Text | References | PDF (1.7 MB) | EPUB
  • 88 Views
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Article
An in-silico approach to understand the potential role of Wnt inhibitory factor-1 (WIF-1) in the inhibition of the Wnt signalling pathway
Plaboni Sen, Suchandra Roy Acharyya, Arisha Arora & Siddhartha Sankar Ghosh
Pages: 326-345
Published online: 30 Mar 2023
AbstractforAn in-silico approach to understand the potential role of Wnt inhibitory factor-1 (WIF-1) in the inhibition of the Wnt signalling pathway | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 359 Views
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Article
Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity
Sadaf Khan & Aabgeena Naeem
Pages: 346-361
Published online: 28 Mar 2023
AbstractforBovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 186 Views
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Article
Hydroxamic acid derivatives as selective HDAC3 inhibitors: computer-aided drug design strategies
Preeti Patel, Sushant Kumar Shrivastava, Piyoosh Sharma, Balak Das Kurmi, Ekta Shirbhate & Harish Rajak
Pages: 362-383
Published online: 30 Mar 2023
AbstractforHydroxamic acid derivatives as selective HDAC3 inhibitors: computer-aided drug design strategies | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 328 Views
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Article
Detection of natural compounds by virtual screening, molecular docking and dynamics studies and evaluation of their effects on tau level in vitro Alzheimer’s model
Ebru Uzunhisarcıklı, İsmail Çelik & Mükerrem Betül Yerer
Pages: 384-392
Published online: 22 Mar 2023
AbstractforDetection of natural compounds by virtual screening, molecular docking and dynamics studies and evaluation of their effects on tau level in vitro Alzheimer’s model | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 385 Views
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Article
Model organism life extending therapeutics modulate diverse nodes in the drug-gene-microbe tripartite human longevity interactome
Rahagir Salekeen, Michael S. Lustgarten, Umama Khan & Kazi Mohammed Didarul Islam
Pages: 393-411
Published online: 27 Mar 2023
AbstractforModel organism life extending therapeutics modulate diverse nodes in the drug-gene-microbe tripartite human longevity interactome | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 491 Views
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Article
Computational analysis and molecular dynamics simulation of high-risk single nucleotide polymorphisms of the ADAM10 gene
Jannatun Nayem Namme, Hasan Mahmud Reza & Asim Kumar Bepari
Pages: 412-424
Published online: 30 Mar 2023
AbstractforComputational analysis and molecular dynamics simulation of high-risk single nucleotide polymorphisms of the ADAM10 gene | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 276 Views
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Article
Comparative analysis of SilA-laccase mediated degradation of ciprofloxacin, norfloxacin and ofloxacin and interpretation of the possible catalytic mechanism
Sunidhi Bhatt, Priyanka Choudhary, Subhankar Chatterjee & Yusuf Akhter
Pages: 425-434
Published online: 25 Apr 2023
AbstractforComparative analysis of SilA-laccase mediated degradation of ciprofloxacin, norfloxacin and ofloxacin and interpretation of the possible catalytic mechanism | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 233 Views
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Article
Fascin − F-actin interaction studied by molecular dynamics simulation and protein network analysis
Xiaodong Wu, Dajia Li, Yang Chen, Liangdong Wang, Li-Yan Xu, En-Min Li & Geng Dong
Pages: 435-444
Published online: 08 Apr 2023
AbstractforFascin − F-actin interaction studied by molecular dynamics simulation and protein network analysis | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 187 Views
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Article
Anxiolytic effects of N-(4,5-dihydro-5-oxo-1,2-dithiolo-[4,3,b]-pyrrole-6-yl)-N-methylformamide, a pyrroloformamide isolated from a marine Streptomyces sp., in adult zebrafish by the 5-HT system
Hozana Patrícia S. de F. Cesário, Francisca Crislândia O. Silva, Maria Kueirislene A. Ferreira, Jane Eire S. A. de Menezes, Hélcio S. dos Santos, Aluísio Marques da Fonseca, Carlos Emídio S. Nogueira, Marcia M. Marinho, Emmanuel S. Marinho, Alexandre Magno R. Teixeira, Edilberto R. Silveira & Otília Deusdênia L. Pessoa
Pages: 445-460
Published online: 10 Apr 2023
AbstractforAnxiolytic effects of N-(4,5-dihydro-5-oxo-1,2-dithiolo-[4,3,b]-pyrrole-6-yl)-N-methylformamide, a pyrroloformamide isolated from a marine Streptomyces sp., in adult zebrafish by the 5-HT system | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 191 Views
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Article
Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer
Sourav Biswas, Md. Rubel Hossen, Shaila Akter, Md. Ackas Ali, Mohammad A. Halim & M. Obayed Ullah
Pages: 461-474
Published online: 30 Mar 2023
AbstractforStructural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 248 Views
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Article
Elucidation of binding mechanism of rhodanine derivative P4OC on bovine serum albumin
Sakthiprabha Sampath, Sangilimuthu Alagar Yadav, Manjunath Meti, Sundaram Kaveri, Ravi Subban & Rajagopal Subramanyam
Pages: 475-482
Published online: 28 Mar 2023
AbstractforElucidation of binding mechanism of rhodanine derivative P4OC on bovine serum albumin | Full Text | References | PDF (1.4 MB) | EPUB
  • 85 Views
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Article
Computer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous α-synuclein fibrils
G. Chandrasekhar, E. Srinivasan, S. Nandhini, G. Pravallika, G. Sanjay & R. Rajasekaran
Pages: 483-494
Published online: 24 Mar 2023
AbstractforComputer aided therapeutic tripeptide design, in alleviating the pathogenic proclivities of nocuous α-synuclein fibrils | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 205 Views
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Article
Screening of potential phytomolecules against MurG as drug target in nosocomial pathogen Pseudomonas aeruginosa: perceptions from computational campaign
Kiran Bharat Lokhande, Sarika Vishnu Pawar, Smriti Madkaiker, Ashish Shrivastava, Swamy K. Venkateswara, Neelu Nawani, Minal Wani, Payel Ghosh & Ashutosh Singh
Pages: 495-508
Published online: 28 Mar 2023
AbstractforScreening of potential phytomolecules against MurG as drug target in nosocomial pathogen Pseudomonas aeruginosa: perceptions from computational campaign | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 196 Views
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Article
Virtual screening and molecular dynamics simulation approach for the identification of potential multi-target directed ligands for the treatment of Alzheimer’s disease
Kailash Jangid, Bharti Devi, Ashrulochan Sahoo, Vijay Kumar, Ashish Ranjan Dwivedi, Suresh Thareja, Rajnish Kumar & Vinod Kumar
Pages: 509-527
Published online: 28 Apr 2023
AbstractforVirtual screening and molecular dynamics simulation approach for the identification of potential multi-target directed ligands for the treatment of Alzheimer’s disease | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 438 Views
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Article
Identification of starvation-mimetic bioactive phytocomponent from Withania somnifera using in-silico molecular modelling and flow cytometry-based analysis for the management of malaria
Deepak Pradhan, Prativa Biswasroy, Sharvari Kulkarni, Rajiv Taliyan, Dilip Kumar Pradhan, Rajesh Kumar Bhola, Sonali Mahapatra, Goutam Ghosh & Goutam Rath
Pages: 528-549
Published online: 23 Apr 2023
AbstractforIdentification of starvation-mimetic bioactive phytocomponent from Withania somnifera using in-silico molecular modelling and flow cytometry-based analysis for the management of malaria | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 111 Views
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Published online: 28 Dec 2023
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