8 results for “Molecular Dynamic Simulation”

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Research ArticleOpen accessIn the keywordsDESIGN OF CANDIDA ANTARCTICA LIPASE B THERMOSTABILITY IMPROVEMENT BY INTRODUCING EXTRA DISULFIDE BOND INTO THE ENZYMEUsman Sumo Friend Tambunan, Ahmad Randy, Arli Aditya ParikesitCandida Antarctica Lipase B (CALB) is extensively studied in enzymatic production of biodiesel, pharmaceutical products, detergents and other chemicals. One drawback of using CALB is its relatively low optimum temperature at 313 K (40°C). The objective of this research is to design CALB mutant with improved thermostability by introducing extra disulfide bond. Molecular dynamic simulation was conducted to get better … …OnLine Journal of Biological Sciences, Vol. 14, Issue 2 · 18 Apr 2014 · 9,492 accessesView PDF Cite

Research ArticleOpen accessIn the abstractUnveiling the Potential of Dombeya buettneri K.Schum As a Drug Agent: Molecular Docking of Compounds With Enzymes Linked to Diabetes and Neurodegenerative DiseaseEsther Emem Nwanna, Samuel Chima Ugbaja et al.This study investigated the mechanisms of Dombeya buettneri (snowball leafy) extracts on diabetes, hypertension, and neurodegenerative diseases. It compared extracts obtained using steep water (a by-product of corn wet milling) and aqueous water. The extracts were analyzed for total phenol, total flavonoid content, antioxidant activities such as FRAP, ABTS, NO, DPPH, iron-induced lipid peroxidation assay, degradation of deoxyribose (Fenton’s reaction), … …OnLine Journal of Biological Sciences, Vol. 25, Issue 4 · 1 Feb 2026 · 2,025 accessesView PDF Cite

Research ArticleOpen accessIn the abstractVirtual Screening of CPP Conjugated Peptide as QcrB BCC Protein Inhibitors of Mycobacterium tuberculosis BacteriaMuhammad Ihsan Muttaqin, Manaman Huang, Usman Sumo Friend TambunanTuberculosis is a global leading cause of death, just below COVID-19 and ranked above HIV. This disease is caused by a pathogen called Mycobacterium tuberculosis, which spreads easily through the air and is known to remain latent in most people's bodies, about a quarter of the world's population. The current problems with TB also include two main concerns: The official … …OnLine Journal of Biological Sciences, Vol. 24, Issue 3 · 14 Mar 2024 · 5,518 accessesView PDF Cite

Research ArticleOpen accessIn the abstractMechanism Analysis of Artemisinin and Artesunate as Lung Cancer Therapy Agents Through in Silico MethodDidik Harmoko, Vivitri Dewi Prasasty, Adi YulandiSeveral in vitro studies have focused on the ability of artemisinin and its derivatives to suppress lung cancer cells, but there are still many biological processes and mechanisms, such as the interactions between the active compounds (ligands) and receptors that are not well understood and require further research. Drug targeting for lung cancer will be more precise and the inhibition … …OnLine Journal of Biological Sciences, Vol. 24, Issue 3 · 15 Feb 2024 · 6,144 accessesView PDF Cite

Research ArticleOpen accessIn the abstractIdentification 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 PDF Cite

Research ArticleOpen accessIn the abstractMolecular Dynamics Simulation of DENV RNA-Dependent RNA-Polymerase with Potential Inhibitor of Disulfide Cyclic PeptideUsman Sumo Friend Tambunan, Raima Syahidah Noors, Arli Aditya Parikesit et al.Problem statement: Our researches have proposed two ligands of disulfide cyclic polypeptide, which are CDEEC and CDGSC as potential inhibitor of DENV RNA-dependent RNApolymerase by molecular docking. Approach: Methodological approach was conducted to determine the best ligand to act as inhibitor. Molecular docking simulation was conducted without a solvent in which enzyme was made rigid and ligand was left free … …OnLine Journal of Biological Sciences, Vol. 11, Issue 2 · 30 Sep 2011 · 8,441 accessesView PDF Cite

Research ArticleOpen accessIn the abstractMolecular Dynamics Studies of Human β-GlucuronidaseIbrahim Ali Noorbatcha, Ayesha Masrur Khan, Hamzah Mohd SallehProblem statement: The enzyme β-glucuronidase is being used as a reporter molecule in the area of genetic engineering, as a component of prodrug therapy in cancer treatment and in the scouring process of cotton fabrics. However, a detailed understanding of the factors responsible for the stability and the activity of this enzyme is still not available. Molecular Dynamics (MD) simulations … …American Journal of Applied Sciences, Vol. 7, Issue 6 · 30 Jun 2010 · 7,613 accessesView PDF Cite

Research ArticleOpen accessAll words, across the recordComputing MDR-Game with Applications to Real DataJimbo Henri Claver, Takeru Suzuki, Jesus Pascal et al.Originally developed for probability and statistic purposes, Multiple Dice Rolling (MDR) game turns out to be useful for many other applications such as complex biological systems and medical research. It has been mainly used to estimate system states that cannot be observed directly. MDR game is affected by noise and fluctuations. It is widely agreed that noise in dynamic systems … …Journal of Computer Science, Vol. 14, Issue 7 · 17 Jul 2018 · 7,789 accessesView PDF Cite