Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 21 (2023)

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Journal of Biomolecular Structure and Dynamics, Volume 41, Issue 21 (2023)

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Research Articles

Article
Identification and exploration of quinazoline-1,2,3-triazole inhibitors targeting EGFR in lung cancer
Sunil Kumar, Sounok Sengupta, Iqra Ali, Manoj K. Gupta, H. Lalhlenmawia, Shavkatjon Azizov & Deepak Kumar
Pages: 11353-11372
Published online: 28 Apr 2023
AbstractforIdentification and exploration of quinazoline-1,2,3-triazole inhibitors targeting EGFR in lung cancer | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 279 Views
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Article
Citrus nutraceutical eriocitrin and its metabolites are partial agonists of peroxisome proliferator-activated receptor gamma (PPARγ): a molecular docking and molecular dynamics study
Mahesha Gangadhariah, Triveni Pardhi, Jahnavi Ravilla, Subhash Chandra & Sridevi Annapurna Singh
Pages: 11373-11393
Published online: 28 Dec 2022
AbstractforCitrus nutraceutical eriocitrin and its metabolites are partial agonists of peroxisome proliferator-activated receptor gamma (PPARγ): a molecular docking and molecular dynamics study | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 171 Views
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Article
Dynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models
Gatta K. R. S. Naresh & Lalitha Guruprasad
Pages: 11394-11414
Published online: 02 Jan 2023
AbstractforDynamic conformational states of apo, ATP and cabozantinib bound TAM kinases to differentiate active-inactive kinetic models | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 141 Views
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Article
Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function
Khadijeh Ahmadi, Behzad Shahbazi, Abdul-Jabbar Zakeri & Hamed Gouklani
Pages: 11415-11430
Published online: 28 Dec 2022
AbstractforCharacterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function | Full Text | References | PDF (2.5 MB) | EPUB
  • 157 Views
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Article
Inhibition of mecA and blaCTX-M from MRSA and ESBL strains of diabetic foot infection by screening antibiotics compound library: an in silico analysis
Sugandhi Pugazhendhi, Thandeeswaran Murugesan, Anand Raj Dhanapal, Ajithkumar Balakrishnan, Baskar Venkidasamy, Hemamalini Vedagiri & Dorairaj Arvind Prasanth
Pages: 11431-11436
Published online: 04 Jan 2023
AbstractforInhibition of mecA and blaCTX-M from MRSA and ESBL strains of diabetic foot infection by screening antibiotics compound library: an in silico analysis | Full Text | References | PDF (895.3 KB) | EPUB | Supplemental
  • 160 Views
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Article
Identification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg12O12 and Zn12O12 nanoclusters: an in silico strategy for COVID-19 treatment
Riyadh Ahmed Atto Al-Shuaeeb, H.R. Abd El-Mageed, Shimaa A. Ahmed, Hussein S. Mohamed, Zeinab S. Hamza, Md. Oliullah Rafi & Md. Shahedur Rahman
Pages: 11437-11449
Published online: 02 Jan 2023
AbstractforIdentification of potent COVID-19 main protease inhibitors by loading of favipiravir on Mg12O12 and Zn12O12 nanoclusters: an in silico strategy for COVID-19 treatment | Full Text | References | PDF (2.5 MB) | EPUB
  • 120 Views
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Article
Design, synthesis, anti-acetylcholinesterase evaluation and molecular modelling studies of novel coumarin-chalcone hybrids
Aso Hameed Hasan, Sonam Shakya, Faiq H.S. Hussain, Sankaranarayanan Murugesan, Subhash Chander, Mohammad Rizki Fadhil Pratama, Shajarahtunnur Jamil, Basundhara Das, Subhrajit Biswas & Joazaizulfazli Jamalis
Pages: 11450-11462
Published online: 02 Jan 2023
AbstractforDesign, synthesis, anti-acetylcholinesterase evaluation and molecular modelling studies of novel coumarin-chalcone hybrids | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 228 Views
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Article
Design of a dual-function agent by fusing a designed anti-VEGF-A binder and CPG-2 enzyme
Ali Etemadi, Mohammad Hossein Karimi-Jafari, Babak Negahdari, Yazdan Asgari, Mohammad Reza Khorramizadeh, Farideh Mohammadian & Mohammadali Mazloomi
Pages: 11463-11470
Published online: 11 Jan 2023
AbstractforDesign of a dual-function agent by fusing a designed anti-VEGF-A binder and CPG-2 enzyme | Full Text | References | PDF (1.3 MB) | EPUB
  • 108 Views
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Article
Molecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma
Vildan Bozok Cetintas, Zekeriya Duzgun, Taner Akalin, Erkin Ozgiray, Eda Dogan, Zafer Yildirim, Nevhis Akinturk, Huseyin Biceroglu, Yesim Ertan & Buket Kosova
Pages: 11471-11483
Published online: 02 Jan 2023
AbstractforMolecular dynamic simulation and functional analysis of pathogenic PTEN mutations in glioblastoma | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 346 Views
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Article
Molecular docking and dynamics supported investigation of antiviral activity of Lichen metabolites of Roccella montagnei: an in silico and in vitro study
Nishanth B. Bhat, Subham Das, Balireddy V. S. Sridevi, Raghu Chandrashekhar H, Sanjeeva Nayaka, Narasimhan S, Sumit Raosaheb Birangal, G. Gautham Shenoy & Alex Joseph
Pages: 11484-11497
Published online: 20 Feb 2023
AbstractforMolecular docking and dynamics supported investigation of antiviral activity of Lichen metabolites of Roccella montagnei: an in silico and in vitro study | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 313 Views
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Article
Molecular dynamics simulation and structural analysis of aquaporin Z from an Antarctic Pseudomonas sp. strain AMS3
S. Balakrishnan, R. N. Z. R. A. Rahman, N. D. M. Noor, W. Latip & M. S. M. Ali
Pages: 11498-11509
Published online: 04 Jan 2023
AbstractforMolecular dynamics simulation and structural analysis of aquaporin Z from an Antarctic Pseudomonas sp. strain AMS3 | Full Text | References | PDF (2.9 MB) | EPUB
  • 100 Views
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Article
The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question
Rayla Kelly Magalhães Costa, Lucas Miguel Pereira Souza, Rudielson Santos Silva, Felipe Rodrigues Souza & André Silva Pimentel
Pages: 11510-11517
Published online: 30 Jan 2023
AbstractforThe reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 154 Views
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Article
Synthesis, characterization, molecular dynamic simulation, and biological assessment of cinnamates linked to imidazole/benzimidazole as a CYP51 inhibitor
Ajayrajsinh R. Zala, Dhanji P. Rajani, Iqrar Ahmad, Harun Patel & Premlata Kumari
Pages: 11518-11534
Published online: 24 Jan 2023
AbstractforSynthesis, characterization, molecular dynamic simulation, and biological assessment of cinnamates linked to imidazole/benzimidazole as a CYP51 inhibitor | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 361 Views
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Article
Discovery of new quinoline and isatine derivatives as potential VEGFR-2 inhibitors: design, synthesis, antiproliferative, docking and MD simulation studies
Mohammed S. Taghour, Hazem Elkady, Wagdy M. Eldehna, Nehal El-Deeb, Ahmed M. Kenawy, Abeer E Abd El-Wahab, Eslam B. Elkaeed, Bshra A. Alsfouk, Ahmed M. Metwaly & Ibrahim H. Eissa
Pages: 11535-11550
Published online: 08 Jan 2023
AbstractforDiscovery of new quinoline and isatine derivatives as potential VEGFR-2 inhibitors: design, synthesis, antiproliferative, docking and MD simulation studies | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 219 Views
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Article
Interactions between β-cyclodextrin as a carrier for anti-cancer drug delivery: a molecular dynamics simulation study
Tahereh Boroushaki & Mohammad G. Dekamin
Pages: 11551-11563
Published online: 04 Jan 2023
AbstractforInteractions between β-cyclodextrin as a carrier for anti-cancer drug delivery: a molecular dynamics simulation study | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 263 Views
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Article
Naphthoquinones biflorin and bis-biflorin (Capraria biflora) as possible inhibitors of the fungus Candida auris polymerase: molecular docking, molecular dynamics, MM/GBSA calculations and in silico drug-likeness study
Aluísio Marques da Fonseca, Neidelenio Baltazar Soares, Regilany Paulo Colares, Mauro Macedo de Oliveira, Larissa Santos Oliveira, Gabrielle Silva Marinho, Mira Raya Paula de Lima, Matheus Nunes da Rocha, Hélcio Silva dos Santos & Emmanuel Silva Marinho
Pages: 11564-11577
Published online: 04 Jan 2023
AbstractforNaphthoquinones biflorin and bis-biflorin (Capraria biflora) as possible inhibitors of the fungus Candida auris polymerase: molecular docking, molecular dynamics, MM/GBSA calculations and in silico drug-likeness study | Full Text | References | PDF (2.5 MB) | EPUB
  • 323 Views
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Article
Synthesis, crystal structure, DFT, Hirshfeld surface analysis, energy framework, docking and molecular dynamic simulations of (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one as anticancer agent
Fouad El Kalai, Emine Berrin Çınar, Yusuf Sert, Mustafa Alhaji Isa, Chin-Hung Lai, Fatimah Buba, Necmi Dege, Noureddine Benchat & Khalid Karrouchi
Pages: 11578-11597
Published online: 09 Jan 2023
AbstractforSynthesis, crystal structure, DFT, Hirshfeld surface analysis, energy framework, docking and molecular dynamic simulations of (E)-4-(4-methylbenzyl)-6-styrylpyridazin-3(2H)-one as anticancer agent | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 281 Views
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Article
Structural and functional characterization of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from Acinetobacter baumannii: identification of promising lead molecules from virtual screening, molecular docking and molecular dynamics simulations
Mahrukh Parveez Zia, Ekampreet Singh, Monika Jain, Jayaraman Muthukumaran & Amit Kumar Singh
Pages: 11598-11611
Published online: 08 Feb 2023
AbstractforStructural and functional characterization of 1-deoxy-D-xylulose-5-phosphate synthase (DXS) from Acinetobacter baumannii: identification of promising lead molecules from virtual screening, molecular docking and molecular dynamics simulations | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 191 Views
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Article
Robust anti-inflammatory activity of genistein against neutrophil elastase: a microsecond molecular dynamics simulation study
Smruti Sudha Nayak & Vino Sundararajan
Pages: 11612-11628
Published online: 27 Jan 2023
AbstractforRobust anti-inflammatory activity of genistein against neutrophil elastase: a microsecond molecular dynamics simulation study | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 162 Views
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Rapid Communication
In silico scanning of structural and functional deleterious nsSNPs in Arabidopsis thaliana’s SOG1 protein, using molecular dynamic simulation approaches
Asif Khan, Muhammad Waqas, Muhammad Tufail, Sobia Ahsan Halim, Waheed Murad, Syed Umair Ahmad, Muhammad Faheem, Jalal Uddin, Asaad Khalid, Ashraf N. Abdalla, Ajmal Khan & Ahmed Al-Harrasi
Pages: 11629-11646
Published online: 03 Feb 2023
AbstractforIn silico scanning of structural and functional deleterious nsSNPs in Arabidopsis thaliana’s SOG1 protein, using molecular dynamic simulation approaches | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 243 Views
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Article
Aloin A inhibits SARS CoV-2 replication by targeting its binding with ACE2 - Evidence from modeling-supported molecular dynamics simulation
Hani A. Alhadrami, Ahmed M. Sayed, Hossam M. Hassan & Mostafa E. Rateb
Pages: 11647-11656
Published online: 08 Feb 2023
AbstractforAloin A inhibits SARS CoV-2 replication by targeting its binding with ACE2 - Evidence from modeling-supported molecular dynamics simulation | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 130 Views
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Article
Design of novel anti-cancer drugs targeting TRKs inhibitors based 3D QSAR, molecular docking and molecular dynamics simulation
Mohammed Er-rajy, Mohamed El fadili, Somdutt Mujwar, Sara Zarougui & Menana Elhallaoui
Pages: 11657-11670
Published online: 25 Jan 2023
AbstractforDesign of novel anti-cancer drugs targeting TRKs inhibitors based 3D QSAR, molecular docking and molecular dynamics simulation | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 267 Views
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Article
GB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction
Krzysztof Kuczera, Robert Szoszkiewicz, Christopher L. Shaffer & Gouri S. Jas
Pages: 11671-11680
Published online: 02 Jan 2023
AbstractforGB1 hairpin kinetics: capturing the folding pathway with molecular dynamics, replica exchange and optimal dimensionality reduction | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 188 Views
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Article
New2-((2-(2,4-dinitrophenyl)hydrazineeylidene) derivatives: design, synthesis, in silico, and in vitro anticancer studies
Vinodkumar P. Sajjan, Lakkappa B. Anigol, Prabhuodeyara M. Gurubasavaraj, Dhanashree Patil, Parutagouda Shankaragouda Patil, Neelamma B. Gummagol, Ching Kheng Quah, Qin Ai Wong & Ismail Celik
Pages: 11681-11699
Published online: 05 Jan 2023
AbstractforNew2-((2-(2,4-dinitrophenyl)hydrazineeylidene) derivatives: design, synthesis, in silico, and in vitro anticancer studies | Full Text | References | PDF (3.4 MB) | EPUB | Supplemental
  • 220 Views
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Article
A knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition
Hossein Lanjanian, Shadi Hosseini, Zahra Narimani, Sogol Meknatkhah & Gholam Hossein Riazi
Pages: 11700-11713
Published online: 09 Jan 2023
AbstractforA knowledge-based protein-protein interaction inhibition (KPI) pipeline: an insight from drug repositioning for COVID-19 inhibition | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 121 Views
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Article
An immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV)
Sarbani Mishra, Madhusmita Rout, Sunita Panda, Susheel Kumar Singh, Rohan Sinha, Budheswar Dehury & Sanghamitra Pati
Pages: 11714-11727
Published online: 02 Jan 2023
AbstractforAn immunoinformatic approach towards development of a potent and effective multi-epitope vaccine against monkeypox virus (MPXV) | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 241 Views
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Article
Design, synthesis, spectroscopic characterizations, single crystal X-ray analysis, in vitro xanthine oxidase and acetylcholinesterase inhibitory evaluation as well as in silico evaluation of selenium-based N-heterocyclic carbene compounds
Gülşen Kaya, Samir Abbas Ali Noma, Duygu Barut Celepci, İmren Bayıl, Tugba Taskin-Tok, Yetkin Gök, Burhan Ateş, Aydın Aktaş, Muhittin Aygün & Burcu Tezcan
Pages: 11728-11747
Published online: 09 Jan 2023
AbstractforDesign, synthesis, spectroscopic characterizations, single crystal X-ray analysis, in vitro xanthine oxidase and acetylcholinesterase inhibitory evaluation as well as in silico evaluation of selenium-based N-heterocyclic carbene compounds | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 431 Views
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Article
In silico design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2
Fatemeh Bayani, Negin Safaei Hashkavaei, Mohammad Reza Karamian, Vuk Uskoković & Yahya Sefidbakht
Pages: 11748-11762
Published online: 26 Jan 2023
AbstractforIn silico design of a multi-epitope vaccine against the spike and the nucleocapsid proteins of the Omicron variant of SARS-CoV-2 | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 294 Views
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Article
pH modulates the role of SP6 RNA polymerase in transcription process: an in silico study
Satya Ranjan Singh & Ayaluru Murali
Pages: 11763-11780
Published online: 29 Jan 2023
AbstractforpH modulates the role of SP6 RNA polymerase in transcription process: an in silico study | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 261 Views
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Article
Vitamin derivatives as potential drugs for Influenza Hemagglutinin
Ananyaa Agrawal, Pratibha Chanana, Vikas Yadav, Vilakshan Bhutani, Naidu Subbarao & Aradhana Srivastava
Pages: 11781-11795
Published online: 11 Jan 2023
AbstractforVitamin derivatives as potential drugs for Influenza Hemagglutinin | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 137 Views
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Article
Comparison of the ligand binding site of C1 domains: a molecular dynamics simulation study of the C1 domain–phorbol 13-acetate–membrane system
Youngki You, Kavya Mathukumalli & Joydip Das
Pages: 11796-11809
Published online: 05 Jan 2023
AbstractforComparison of the ligand binding site of C1 domains: a molecular dynamics simulation study of the C1 domain–phorbol 13-acetate–membrane system | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 157 Views
  • 2 CrossRef citations
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Article
Structural dynamics and susceptibility of isobutylamido thiazolyl resorcinol (ThiamidolTM) against human and mushroom tyrosinases
Panupong Mahalapbutr, Napat Nuramrum, Thanyada Rungrotmongkol, Napat Kongtaworn & Sahachai Sabuakham
Pages: 11810-11817
Published online: 16 Jan 2023
AbstractforStructural dynamics and susceptibility of isobutylamido thiazolyl resorcinol (ThiamidolTM) against human and mushroom tyrosinases | Full Text | References | PDF (1.9 MB) | EPUB
  • 328 Views
  • 1 CrossRef citations
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Article
In silico drug screen reveals potential competitive MTHFR inhibitors for clinical repurposing
Nazlıgül Keske, Başak Özay, Ezgi Yağmur Tükel, Muratcan Menteş & Cihangir Yandım
Pages: 11818-11831
Published online: 04 Jan 2023
AbstractforIn silico drug screen reveals potential competitive MTHFR inhibitors for clinical repurposing | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 404 Views
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Article
In vitro anticancer, antioxidant and enzyme inhibitory potentials of endemic Cephalaria elazigensis var. purpurea with in silico studies
Mehmet Kadir Erdogan, Ramazan Gundogdu, Yakup Yapar, Ibrahim Halil Gecibesler, Mahinur Kirici, Lutfi Behcet, Burak Tüzün, Tugba Taskin-Tok & Parham Taslimi
Pages: 11832-11844
Published online: 13 Jan 2023
AbstractforIn vitro anticancer, antioxidant and enzyme inhibitory potentials of endemic Cephalaria elazigensis var. purpurea with in silico studies | Full Text | References | PDF (2.7 MB) | EPUB
  • 335 Views
  • 4 CrossRef citations
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Article
Cell cycle kinases (AUKA, CDK1, PLK1) are prognostic biomarkers and correlated with tumor-infiltrating leukocytes in HBV related HCC
Baitul Islam, Hai-Yang Yu, Tian-Qi Duan, Jing Pan, Min Li, Ru-Qi Zhang, Matiullah Masroor & Ju-Fang Huang
Pages: 11845-11861
Published online: 12 Jan 2023
AbstractforCell cycle kinases (AUKA, CDK1, PLK1) are prognostic biomarkers and correlated with tumor-infiltrating leukocytes in HBV related HCC | Full Text | References | PDF (4.1 MB) | EPUB
  • 228 Views
  • 1 CrossRef citations
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Article
Virtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A
Smriti Singh, Papia Chowdhury, Arabinda Ghosh & Seema Nara
Pages: 11862-11871
Published online: 04 Jan 2023
AbstractforVirtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 257 Views
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Article
Phenolic compounds from Tradescantia pallida ameliorate diabetes by inhibiting enzymatic and non-enzymatic pathways
Fariha Imtiaz, Muhammad Islam, Hamid Saeed & Abrar Ahmed
Pages: 11872-11888
Published online: 04 Jan 2023
AbstractforPhenolic compounds from Tradescantia pallida ameliorate diabetes by inhibiting enzymatic and non-enzymatic pathways | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 232 Views
  • 2 CrossRef citations
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Article
Identification of deleterious nsSNPs in human HGF gene: in silico approach
Anila Hoda, Mirela Lika (Çekani)Valbona Kolaneci
Pages: 11889-11903
Published online: 04 Jan 2023
AbstractforIdentification of deleterious nsSNPs in human HGF gene: in silico approach | Full Text | References | PDF (2.6 MB) | EPUB
  • 229 Views
  • 3 CrossRef citations
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Article
Discovery and optimization of natural-based nanomolar c-Kit inhibitors via in silico and in vitro studies
Hossam Nada, Sungdo Kim, Sreenivasulu Godesi, Joohan Lee & Kyeong Lee
Pages: 11904-11915
Published online: 12 Jan 2023
AbstractforDiscovery and optimization of natural-based nanomolar c-Kit inhibitors via in silico and in vitro studies | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 131 Views
  • 6 CrossRef citations
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Article
Scaffold identification and drug repurposing for finding potential Dengue envelope inhibitors through ligand-based pharmacophore model
Sasi Priya, Vidya Jyothi Alli & Surender Singh Jadav
Pages: 11916-11929
Published online: 29 Jan 2023
AbstractforScaffold identification and drug repurposing for finding potential Dengue envelope inhibitors through ligand-based pharmacophore model | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 190 Views
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Article
Integrated LC-MS/MS and network pharmacology approach for predictingactive ingredients and pharmacological mechanisms of Tribulus terrestris L. against cardiac diseases
Chigateri M. Vinay, Chetan Hasmukh Mehta, Chandrakanth Bhat, Archana Kamath, Manjunath B Joshi, Bobby Paul, Usha Yogendra Nayak & Padmalatha S. Rai
Pages: 11930-11945
Published online: 12 Apr 2023
AbstractforIntegrated LC-MS/MS and network pharmacology approach for predictingactive ingredients and pharmacological mechanisms of Tribulus terrestris L. against cardiac diseases | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 940 Views
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Article
Analogue and structure based approaches for modelling HIV-1 integrase inhibitors
Anurag Upadhyaya, Bhavana Panthi, Shubham Verma, Suresh Kumar, Satish Kumar Rajouria, Hemant Kumar Srivastava & Pranjal Chandra
Pages: 11946-11956
Published online: 03 Feb 2023
AbstractforAnalogue and structure based approaches for modelling HIV-1 integrase inhibitors | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 103 Views
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Article
Discovering potential stabilizers for KRAS22RT G-quadruplex DNA: an alternative next generation approach to treat pancreatic cancer
Maha Yousaf, Dua Fatima, Javaria Amin, Aqsa Noureen & Muhammad Qaiser Fatmi
Pages: 11957-11968
Published online: 02 Feb 2023
AbstractforDiscovering potential stabilizers for KRAS22RT G-quadruplex DNA: an alternative next generation approach to treat pancreatic cancer | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 264 Views
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Article
Structural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network
Datta Darshan V. M.Venketesh Sivaramakrishnan & K. Arvind Kumar
Pages: 11969-11986
Published online: 08 Jan 2023
AbstractforStructural systems biology approach delineate the functional implications of SNPs in exon junction complex interaction network | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 244 Views
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Article
Hybrids of thiazolidinone with 1,2,3-triazole derivatives: design, synthesis, biological evaluation, in silico studies, molecular docking, molecular dynamics simulations, and ADMET profiling
Abdoullah Bimoussa, Mourad Fawzi, Ali Oubella, Syeda Abida Ejaz, Muhammad Sajjad Bilal, Mohamed Labd Taha, Aziz Auhmani, Hamid Morjani, Anthony Robert, Abdelkhalek Riahi & My Youssef Ait Itto
Pages: 11987-11999
Published online: 09 Jan 2023
AbstractforHybrids of thiazolidinone with 1,2,3-triazole derivatives: design, synthesis, biological evaluation, in silico studies, molecular docking, molecular dynamics simulations, and ADMET profiling | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 231 Views
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Article
Druggable sites identification in Streptococcus mutans VicRK system evaluated by catechols
Paulo Henrique Santana Silveira & Samuel Silva da Rocha Pita
Pages: 12000-12015
Published online: 26 Jan 2023
AbstractforDruggable sites identification in Streptococcus mutans VicRK system evaluated by catechols | Full Text | References | PDF (2.2 MB) | EPUB
  • 137 Views
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Article
Signaling landscape of mitochondrial non-coding RNAs
Gnanavel Mutharasu, Akshaya Murugesan, Saravnan Kondamani, Ramesh Thiyagarajan, Olli Yli-Harja & Meenakshisundaram Kandhavelu
Pages: 12016-12025
Published online: 09 Jan 2023
AbstractforSignaling landscape of mitochondrial non-coding RNAs | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 248 Views
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Article
Bergamottin: location, aggregation and interaction with the plasma membrane
José Villalaín
Pages: 12026-12037
Published online: 05 Jan 2023
AbstractforBergamottin: location, aggregation and interaction with the plasma membrane | Full Text | References | PDF (1.5 MB) | EPUB | Supplemental
  • 99 Views
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Article
In silico approach towards polyphenols as targeting glucosamine-6-phosphate synthase for Candida albicans
Sachin Dhawale, Madhuri Pandit, Kanchan Thete, Dnyaneshwari Ighe, Sachin Gawale, Pallavi Bhosle & Deepak K. Lokwani
Pages: 12038-12054
Published online: 11 Jan 2023
AbstractforIn silico approach towards polyphenols as targeting glucosamine-6-phosphate synthase for Candida albicans | Full Text | References | PDF (3.4 MB) | EPUB
  • 222 Views
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Article
Anxiolytic and anticonvulsant effect of Ibuprofen derivative through GABAergic neuromodulation in adult Zebrafish
Tatiana Rodrigues Garcia, Paulo de Tarso Cavalcante Freire, Antonio Wlisses da Silva, Maria Kueirislene Amâncio Ferreira, Emanuela de Lima Rebouças, Francisco Rogênio Silva Mendes, Emanuelle Machado Marinho, Marcia Machado Marinho, Alexandre Magno Rodrigues Teixeira, Emmanuel Silva Marinho, Paulo Nogueira Bandeira, Jane Eire Silva Alencar de Menezes & Helcio Silva dos Santos
Pages: 12055-12062
Published online: 25 Jan 2023
AbstractforAnxiolytic and anticonvulsant effect of Ibuprofen derivative through GABAergic neuromodulation in adult Zebrafish | Full Text | References | PDF (1.2 MB) | EPUB
  • 267 Views
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Article
Identification of potent EGFR-TKD inhibitors from NPACT database through combined computational approaches
Showkat Ahmad Mir, Auwal Muhammad, Archana Padhiary, Nirius Jenen Ekka, Iswar Baitharu, Pradeep Kumar Naik & Binata Nayak
Pages: 12063-12076
Published online: 25 Jan 2023
AbstractforIdentification of potent EGFR-TKD inhibitors from NPACT database through combined computational approaches | Full Text | References | PDF (3.9 MB) | EPUB | Supplemental
  • 167 Views
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Article
Synthesis of thiazole-based-thiourea analogs: as anticancer, antiglycation and antioxidant agents, structure activity relationship analysis and docking study
Muhammad Taha, Fazal Rahim, Ihsan Ullah Khan, Nizam Uddin, Rai Khalid Farooq, Abdul Wadood, Ashfaq Ur Rehman & Khalid Mohammed Khan
Pages: 12077-12092
Published online: 25 Jan 2023
AbstractforSynthesis of thiazole-based-thiourea analogs: as anticancer, antiglycation and antioxidant agents, structure activity relationship analysis and docking study | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 304 Views
  • 1 CrossRef citations
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Article
Immunoinformatics aided approach for predicting potent cytotoxic T cell epitopes of respiratory syncytial virus
Gayathri Anandhan, Yogesh B. Narkhede, Manikandan Mohan & Premasudha Paramasivam
Pages: 12093-12105
Published online: 19 Mar 2023
AbstractforImmunoinformatics aided approach for predicting potent cytotoxic T cell epitopes of respiratory syncytial virus | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 146 Views
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Article
Integrative transcriptome analysis of triple negative breast cancer profiles for identification of druggable targets
Poornima Arumugam, Vignesh Ramesh, Banupriya Sampathkumar, Haribalan Perumalsamy, Sri Renukadevi Balusamy, Kanagaraj Suganya, Sudha Balraj, S. Kumar Nachimuthu & Sumathi Sundaravadivelu
Pages: 12106-12119
Published online: 09 Jan 2023
AbstractforIntegrative transcriptome analysis of triple negative breast cancer profiles for identification of druggable targets | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 315 Views
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Article
Fabrication, characterization and biological properties evaluation of bioactive scaffold based on mineralized carbon nanofibers
Mehdi Azizi, Amin Shavandi, Masoud Hamidi, Shayan Gholizadeh, Mahnaz Mohammadpour, Mohammad Saeid Salami & Hadi Samadian
Pages: 12120-12127
Published online: 16 Jan 2023
AbstractforFabrication, characterization and biological properties evaluation of bioactive scaffold based on mineralized carbon nanofibers | Full Text | References | PDF (1.9 MB) | EPUB
  • 101 Views
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Article
Computational studies on potential small molecule inhibitors of Leishmania pteridine reductase 1
Aaron Boakye, Edward Ntim Gasu, Jehoshaphat Oppong Mensah & Lawrence Sheringham Borquaye
Pages: 12128-12141
Published online: 12 Jan 2023
AbstractforComputational studies on potential small molecule inhibitors of Leishmania pteridine reductase 1 | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 303 Views
  • 4 CrossRef citations
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Article
AlteQ: a new complementarity principle-centered method for the evaluation of docking poses
Shivananda Kandagalla, Maria Grishina, Jurica Novak, Hrvoje Rimac, B. S. Sharath & Vladimir Potemkin
Pages: 12142-12156
Published online: 11 Jan 2023
AbstractforAlteQ: a new complementarity principle-centered method for the evaluation of docking poses | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 98 Views
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Article
Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease
Palanisamy Deepa & Duraisamy Thirumeignanam
Pages: 12157-12170
Published online: 16 Jan 2023
AbstractforUnderstanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 88 Views
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Article
Field and atom-based 3D-QSAR models of chromone (1-benzopyran-4-one) derivatives as MAO inhibitors
Moumita Saha, Shankar Gupta, Shubham Dhiman, Vivek Asati, Amena Ali & Abuzer Ali
Pages: 12171-12185
Published online: 17 Jan 2023
AbstractforField and atom-based 3D-QSAR models of chromone (1-benzopyran-4-one) derivatives as MAO inhibitors | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 187 Views
  • 2 CrossRef citations
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Article
Pharmacophore-based virtual screening and in-silico study of natural products as potential DENV-2 RdRp inhibitors
Miah Roney, A. K. M. Moyeenul Huq, Abdul Rashid Issahaku, Mahmoud E. S. Soliman, Md. Sanower Hossain, Abu Hasnat Mustafa, Md. Alimul Islam, Amit Dubey, Aisha Tufail, Mohd Fadhlizil Fasihi Mohd Aluwi & Saiful Nizam Tajuddin
Pages: 12186-12203
Published online: 16 Jan 2023
AbstractforPharmacophore-based virtual screening and in-silico study of natural products as potential DENV-2 RdRp inhibitors | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 447 Views
  • 7 CrossRef citations
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Article
Potential of plant extracts in targeting SARS-CoV-2 main protease: an in vitro and in silico study
Ingrid Garcia de Araujo, José Renato Pattaro-Júnior, Cecilia Gomes Barbosa, Gisele Strieder Philippsen, Ana Rita Silva, Rafaella Sayuri Ioshino, Carolina Borsoi Moraes, Lúcio Holanda Freitas-Junior, Lillian Barros, Rosane Marina Peralta, Maria Aparecida Fernandez & Flavio Augusto Vicente Seixas
Pages: 12204-12213
Published online: 18 Jan 2023
AbstractforPotential of plant extracts in targeting SARS-CoV-2 main protease: an in vitro and in silico study | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 295 Views
  • 3 CrossRef citations
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Article
Colchicine as potential inhibitor targeting MMP-9, NOX2 and TGF-β1 in myocardial infarction: a combination of docking and molecular dynamic simulation study
Suryono Suryono, Mohammad Saifur Rohman, Edi Widjajanto, Seskoati Prayitnaningsih & Titin Andri Wihastuti
Pages: 12214-12224
Published online: 13 Jan 2023
AbstractforColchicine as potential inhibitor targeting MMP-9, NOX2 and TGF-β1 in myocardial infarction: a combination of docking and molecular dynamic simulation study | Full Text | References | PDF (1.5 MB) | EPUB
  • 246 Views
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Article
In silico prediction of the possible antidiabetic and anti-inflammatory targets of Nymphaea lotus-derived phytochemicals and mechanistic insights by molecular dynamics simulations
Ifeoluwa Temitayo Oyeyemi, Kayode Ezekiel Adewole & Gideon Ampoma Gyebi
Pages: 12225-12241
Published online: 16 Jan 2023
AbstractforIn silico prediction of the possible antidiabetic and anti-inflammatory targets of Nymphaea lotus-derived phytochemicals and mechanistic insights by molecular dynamics simulations | Full Text | References | PDF (2.5 MB) | EPUB
  • 239 Views
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Article
Molecular cloning, expression, mRNA secondary structure and immunological characterization of mussel foot proteins (Mfps) (Mollusca: Bivalvia)
P. P. Anand & Y. Shibu Vardhanan
Pages: 12242-12266
Published online: 23 Jan 2023
AbstractforMolecular cloning, expression, mRNA secondary structure and immunological characterization of mussel foot proteins (Mfps) (Mollusca: Bivalvia) | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 176 Views
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Article
Withanolides of Athenaea velutina with potential inhibitory properties against SARS coronavirus main protease (mpro): molecular modeling studies
Pabllo Abreu Alves, Késya Amanda Dantas Rocha, Lucas Lima Bezerra, Alejandro Pedro Ayala, Norberto de Kássio Vieira Monteiro & Otília Deusdênia Loiola Pessoa
Pages: 12267-12275
Published online: 23 Jan 2023
AbstractforWithanolides of Athenaea velutina with potential inhibitory properties against SARS coronavirus main protease (mpro): molecular modeling studies | Full Text | References | PDF (1.4 MB) | EPUB | Supplemental
  • 171 Views
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Article
Molecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives
Mohd. Akram, Mohammad Osama, Md. Amiruddin Hashmi & Kabir-ud-Din
Pages: 12276-12291
Published online: 25 Jan 2023
AbstractforMolecular interaction of di-ester bonded cationic Gemini surfactants with pepsin: in vitro and in silico perspectives | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 92 Views
  • 1 CrossRef citations
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Article
Computational modeling of cyanobacterial phytoconstituents against toll-like receptors of skin cancer
Elhan Khan, Mahvish Khan, Saif Khan, Mohtashim Lohani, Nashwa Zaki Ali Bushara, Hussein Abdul Aziz Marouf, Kurian Punnoose & Iffat Zareen Ahmad
Pages: 12292-12304
Published online: 06 Feb 2023
AbstractforComputational modeling of cyanobacterial phytoconstituents against toll-like receptors of skin cancer | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 253 Views
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Article
In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA
Mirza Sarwar Baig, Deepanshu, Prem Prakash, Pravej Alam & Anuja Krishnan
Pages: 12305-12327
Published online: 08 Feb 2023
AbstractforIn silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 232 Views
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Article
Identification of HER2 inhibitors from curcumin derivatives using combination of in silico screening and molecular dynamics simulation
Oluwatosin A. Saibu, Gagandeep Singh, Sunday A. Olugbodi, Adenrele T. Oluwafemi, Temitope M. Ajayi, Sodiq O. Hammed, Oladapo O. Oladipo, Tope T. Odunitan & Damilola A. Omoboyowa
Pages: 12328-12337
Published online: 08 Feb 2023
AbstractforIdentification of HER2 inhibitors from curcumin derivatives using combination of in silico screening and molecular dynamics simulation | Full Text | References | PDF (1.6 MB) | EPUB | Supplemental
  • 304 Views
  • 4 CrossRef citations
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Article
HPV and molecular mimicry in systemic lupus erythematosus and an impact of compiling B-cell epitopes and MHC-class II binding profiles with in silico evidence
D. John Dickson Calvin, Runal John Steve, Rajesh Kannangai, Priya Abraham, S. Udhaya Kumar, Ambritha Balasundaram, C. George Priya Doss, Vinotha Thomas, Anitha Thomas, Debashish Danda & John Gnanadurai Fletcher
Pages: 12338-12346
Published online: 06 Feb 2023
AbstractforHPV and molecular mimicry in systemic lupus erythematosus and an impact of compiling B-cell epitopes and MHC-class II binding profiles with in silico evidence | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 231 Views
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Article
Synthesis, structure elucidation, Hirshfeld surface analysis, DFT, and molecular docking of new 6-bromo-imidazo[4,5-b]pyridine derivatives as potential tyrosyl-tRNA synthetase inhibitors
Zainab Jabri, Aravazhi Amalan Thiruvalluvar, Riham Sghyar, Joel T. Mague, Safia Sabir, Youssef Kandri Rodi, El Hassane Anouar, Khalid Misbahi, Nada Kheira Sebbar & El Mokhtar Essassi
Pages: 12347-12362
Published online: 06 Feb 2023
AbstractforSynthesis, structure elucidation, Hirshfeld surface analysis, DFT, and molecular docking of new 6-bromo-imidazo[4,5-b]pyridine derivatives as potential tyrosyl-tRNA synthetase inhibitors | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 121 Views
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Article
Computational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA
Shashi Kumar, Soumya Biswas & Parag A. Deshpande
Pages: 12363-12371
Published online: 06 Feb 2023
AbstractforComputational analysis of the effect of Gly100Ala mutation on the thermostability of SazCA | Full Text | References | PDF (1.2 MB) | EPUB
  • 129 Views
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Article
The allosteric effect of the upper half of SENP1 contributes to its substrate selectivity for SUMO1 over SUMO2
Yuxin Shi, Miersalijiang Yasen, Zhijun Wang, Tingting Du, Yelei Ding, Xuefei Li, Zongtao Chai, Chen Jie, Guanqun Ju & Mingfei Ji
Pages: 12372-12386
Published online: 19 Jan 2023
AbstractforThe allosteric effect of the upper half of SENP1 contributes to its substrate selectivity for SUMO1 over SUMO2 | Full Text | References | PDF (2.4 MB) | EPUB
  • 224 Views
  • 1 CrossRef citations
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Article
The pathogenic effect of SNPs on structure and function of human TLR4 using a computational approach
Priya Prakasam, Abdul Ajees Abdul Salam & Syed Ibrahim Basheer Ahamed
Pages: 12387-12400
Published online: 17 Jan 2023
AbstractforThe pathogenic effect of SNPs on structure and function of human TLR4 using a computational approach | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 258 Views
  • 1 CrossRef citations
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Article
Structural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators
F. Saritha, N. Aiswarya, R. Aswath Kumar & K.V. Dileep
Pages: 12401-12410
Published online: 08 Feb 2023
AbstractforStructural analysis and ensemble docking revealed the binding modes of selected progesterone receptor modulators | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 140 Views
  • 1 CrossRef citations
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Article
The anticancer and EGFR-TK/CDK-9 dual inhibitory potentials of new synthetic pyranopyrazole and pyrazolone derivatives: X-ray crystallography, in vitro, and in silico mechanistic investigations
Arafa Musa, Saleh K. Ihmaid, David L. Hughes, Musa A. Said, Hamada S. Abulkhair, Ahmed H. El-Ghorab, Mohamed A. Abdelgawad, Khaled Shalaby, Mohamed E. Shaker, Khalid Saad Alharbi, Nasser Hadal Alotaibi, Deborah L. Kays, Laurence J. Taylor, Della Grace Thomas Parambi, Sami I. Alzarea, Ahmed A. Al-Karmalawy, Hany E. A. Ahmed & Ahmed M. El-Agrody
Pages: 12411-12425
Published online: 20 Jan 2023
AbstractforThe anticancer and EGFR-TK/CDK-9 dual inhibitory potentials of new synthetic pyranopyrazole and pyrazolone derivatives: X-ray crystallography, in vitro, and in silico mechanistic investigations | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 333 Views
  • 9 CrossRef citations
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Article
GABAA and serotonergic receptors participation in anxiolytic effect of chalcones in adult zebrafish
Francisco Rogênio Silva Mendes, Antonio Wlisses da Silva, Maria Kueirislene Amâncio Ferreira, Emanuela de Lima Rebouças, Italo Moura Barbosa, Matheus Nunes da Rocha, Walber Henrique Ferreira Ribeiro, Ramon Róseo Paula Pessoa Bezerra de Menezes, Emanuel Paula Magalhães, Emanuelle Machado Marinho, Márcia Machado Marinho, Paulo Nogueira Bandeira, Jane Eire Silva Alencar de Menezes, Emmanuel Silva Marinho & Hélcio Silva dos Santos
Pages: 12426-12444
Published online: 16 Jan 2023
AbstractforGABAA and serotonergic receptors participation in anxiolytic effect of chalcones in adult zebrafish | Full Text | References | PDF (2.3 MB) | EPUB | Supplemental
  • 294 Views
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