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42 results for “Molecular Dynamics (MD)”
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Research ArticleOpen accessEvery word in the titleIdentification of Pharmacological Targets Combining Docking and Molecular Dynamics SimulationsIlizaliturri-Flores Ian, Rosas-Trigueros Jorge Luis, Carrillo-Vazquez Jonathan Pablo et al.Studies that include both experimental data and computational simulations (in silico) have increased in number because the techniques are complementary. In silico methodologies are currently an essential component of drug design; moreover, identification and optimization of the best ligand based on the structures of biomolecules are common scientific challenges. Geometric structural properties of biomolecules explain their behavior and interactions and … …American Journal of Agricultural and Biological Sciences, Vol. 8, Issue 1 · 21 Mar 2013 · 8,128 accessesView PDFCite
Research ArticleOpen accessIn the keywordsAdsorption Behavior of Bone Morphogenetic Protein-2 on a Graphite Substrate for Biomedical ApplicationsIzabele Marquetti, Salil DesaiThe interaction of proteins with biomaterials plays an important role for several biomedical applications including implants and tissue engineering. Although different experimental approaches have been explored, the investigation of the molecular models for protein-substrate interaction is warranted to control of cellular functions. In this study, Molecular Dynamics (MD) simulations were used to study the adsorption behavior of Bone Morphogenetic Protein-2 … …American Journal of Engineering and Applied Sciences, Vol. 11, Issue 2 · 19 Jun 2018 · 8,705 accessesView PDFCite
Research ArticleOpen accessIn the keywordsDesigning of Disulfide Cyclic Peptide for Inhibiting Polymerase A and B1 (PAC-PB1N) in H1N1 Virus using Molecular Simulation ApproachUsman Sumo Friend Tambunan, Mochammad Arfin Fardiansyah Nasution, Arli Aditya Parikesit et al.The drug resistance A/H1N1 flu virus is emerging rapidly. Therefore, looking for potential therapy is very important. PB2, PB and PA are subunits of viral RNA-dependent RNA polymerase (RdRp). They play an important role in viral replication. The PA and PB1 binding sites can be considered as potential targets for the development of new influenza drugs. The peptide inhibitors can … …OnLine Journal of Biological Sciences, Vol. 16, Issue 3 · 24 Aug 2016 · 7,310 accessesView PDFCite
Research ArticleOpen accessIn the keywordsIn-silico Rational Protein Engineering and Design Approach to Improve Thermostability of a Haloalkane Dehalogenase EnzymeRaghunath Satpathy, V. Badireenath Konkimalla, Jagnyeswar RathaThermostability of enzymes is a major prerequisite for use in industrial enzymology. There are as such no simple general principles for achieving thermostability in case of enzymes as many factors are required to fulfil for different enzymes. The present study describes computational methods to design thermostable haloalkane dehalogenase enzyme using the crystal structure available Protein Data Bank (PDB ID: 1EDE). … …Current Research in Bioinformatics, Vol. 4, Issue 2 · 13 Oct 2015 · 8,279 accessesView PDFCite
Research ArticleOpen accessIn the keywordsIN SILICO DESIGN OF THE M2 PROTON CHANNEL INHIBITORS OF H1N1 VIRUSUsman Sumo Friend Tambunan, Mochamad Reza Rahdiansyah, Arli Aditya ParikesitM2 proton channel of H1N1 Influenza A virus is the target protein anti-flu drugs amantadine and rimantadine. However, the two once powerful adamantane-based drugs lost their 90% bioactivity because of mutations of virus in recent twenty years. The resistance of influenza A virus to amantadine need to develop more effective adamantane-based drugs. Several research by molecular docking method have been … …OnLine Journal of Biological Sciences, Vol. 13, Issue 1 · 5 Jan 2013 · 7,999 accessesView PDFCite
Research ArticleOpen accessIn the keywordsIn silico and in vitro Structural Analysis on the Interaction of Calmodulin and Calmodulin-Binding Motif of FKBP35 from Plasmodium knowlesiSazlinawatie Aladin, Cahyo Budiman et al.FK506-binding protein 35 (FKBP35) is a peptidyl-prolyl cis-trans isomerase found in Plasmodium knowlesi, a zoonotic malaria parasite responsible for concerning cases of malaria infection in East Malaysia. This protein contains a segment known as the calmodulin-binding motif (Pk-CBM), which is predicted to facilitate interaction with calmodulin from P. knowlesi (Pk-CaM). Although this interaction is considered promising for future antimalarial drug … …OnLine Journal of Biological Sciences, Vol. 25, Issue 2 · 10 Mar 2025 · 4,846 accessesView PDFCite
Research ArticleOpen accessIn the abstractVirtual Screening of Bioactive Compounds from the Onion (Allium) Genus as Potential Epidermal Growth Factor Receptor Inhibitors for MonkeypoxDinda Ratu Agustiani, Rakhmat Ramdhani Alwie, Harry NoviardiMonkeypox (Mpox) is an emerging zoonotic disease caused by the Mpox virus infection that affects humans and animals. Epidermal Growth Factor Receptor (EGFR) is an important target in the pathogenesis of Mpox. Epidermal Growth Factor (EGF), encoded by orthopoxviruses, plays an important role in intercellular transmission of the virus. Onion is known to have antiviral and immunomodulatory properties. Active compounds … …OnLine Journal of Biological Sciences, Vol. 26, Issue 3 · 6 Aug 2026 · 945 accessesView PDFCite
Research ArticleOpen accessIn the abstractImpact of Integrated Nursing and Digital Droplet PCR on Bullous Dermatoid Conditions: A Randomized Controlled TrialConghui ChenBullous skin disease is an autoimmune disease characterized by the formation of blisters on the skin or mucous membrane, which seriously impairs the quality of life and overall health. Similar to the research on biomolecules (mechanics of protein interaction), cells (including cell membrane elasticity, cell adhesion, cytoskeletal dynamics, response to mechanical stimulation, cell deformation and cell endoforce transfer) and tissue … …American Journal of Biochemistry and Biotechnology, Vol. 22, Issue 2 · 2 Jul 2026 · 985 accessesView PDFCite
Research ArticleOpen accessIn the abstractCytotoxicity Evaluation of Curcumin-FITC Conjugates in Granulosa Cells Isolated from Ovarian Follicles of Kampung Chicken (Gallus gallus domesticus)Sukarman Hadi Jaya Putra, Mansur S, UmarudinLinking curcumin to fluorescein isothiocyanate (FITC) results in a hybrid fluorescent marker (curcumin-FITC) that exhibits improved stability and sensitivity in detection. This study sought to evaluate the biological safety and cytotoxic effects of curcumin-FITC on granulosa cells obtained from ovarian follicles (2-5 mm, F1-F4 stage) of Kampung chickens. Following fluorescent labeling with different concentrations of curcumin-FITC (0-100 μg/mL), cell viability … …OnLine Journal of Biological Sciences, Vol. 26, Issue 2 · 14 May 2026 · 1,497 accessesView PDFCite
Research ArticleOpen accessIn the abstractDecoding Lung Cancer: PLAU as a Critical Driver and Diagnostic MarkerStanley Cho, Min Gyeong KimLung cancer remains a leading cause of cancer-related mortality, and understanding its underlying molecular mechanisms is critical for developing targeted therapies. We developed a novel tool called the Transcriptome-TCGA Integration (TTI), which combines in vitro transcriptome data with clinical datasets from the Cancer Genome Atlas (TCGA). TTI allows for the identification of key genes and pathways involved in lung cancer, … …OnLine Journal of Biological Sciences, Vol. 25, Issue 4 · 15 Feb 2026 · 1,424 accessesView PDFCite