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43 articles for “docking”
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Research ArticleOpen accessIn the keywordsMechanism 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 PDFCite
Research ArticleOpen accessIn the keywordsApoptosis in Yeast is Modulated by Clove Leaf Extract and Eugenol Potentially by Interfering Caspase YCA1Septyani Amini, Rika Indri Astuti, Irmanida BatubaraApoptosis is a process of cell death important for preventing the development of diseases such as cancer, neurodegenerative disorders, autoimmune, and cardiovascular disease. Apoptosis is reported to be potentially induced by antioxidant compounds, including phytoextract. Thus in this study, we determined the potential of apoptotic modulation in yeast cells by clove extract, which was rich in eugenol. Apoptotic in yeast … …OnLine Journal of Biological Sciences, Vol. 22, Issue 3 · 15 Sep 2022 · 5,497 accessesView PDFCite
Research ArticleOpen accessIn the keywordsStructural and Substrate Interaction Properties of Alkaline Phosphatase from Paenibacillus sp. PSB04: In-Silico AnalysisHerman Umbau Lindang, Cahyo BudimanA Phosphate-Solubilising Bacterium (PSB) of Paenibacillus sp. PSB04 was previously isolated from the Sabah tropical rainforest in Malaysia. Interestingly, the genome sequence of the PSB04 strain harbored an Alkaline Phosphatase (AP) (EC 3.1.3.1) gene and was hypothesized to have unique structural characteristics. Therefore, this study aims to determine the AP three-Dimensional (3D) model and catalytic mechanism from Paenibacillus sp. PSB04 … …OnLine Journal of Biological Sciences, Vol. 22, Issue 3 · 16 Jul 2022 · 5,910 accessesView PDFCite
Research ArticleOpen accessIn the keywordsIn Silico Cholinesterase and Monoamine Oxidase Inhibitory Activities of Perillaldehyde and D-Limonene, Main Compounds of Essential Oil of Algerian Ammodaucus leucotrichusNesrine Sadaoui-Smadhi, Souad Khemili-Talbi, Wadood Abdul et al.In a continuation of our previous work for the exploration of novel enzyme inhibitors, molecular modeling was used to inspect the binding mode of perillaldehyde and D-limonene, the major compounds of essential oil of Algerian Ammodaucus leucotrichus into the active site pocket of cholinesterase (AChE and BuChE) and Monoamine Oxidase (MAO). The molecular docking was carried out using Molecular Operating … …Current Research in Bioinformatics, Vol. 8, Issue 1 · 28 Feb 2020 · 7,313 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 keywordsStructure Prediction and Binding Site Analysis of Hepatotoxic Microcystin-LR Degrading MlrC-Like Protein from Burkholderia sp. using Computational ApproachesDhananjaya P. Singh, Ratna Prabha, Vivek Keshri, P.C. AbhilashMicrocystin-LR (MCYST-LR) is a well characterized hepatotoxic heptapeptide produced by various species of cyanobacteria including Microcystis aeruginosa. Burkholderia is a genus of bacteria with cyanobacterial toxins degrading property. This study predicts the structure of microcystin degrading MlrC-like protein from Burkholderia sp. strain CCGE1002 that has microcystin degradation capability. Binding interaction of MlrC-like protein with MCYST-LR was studied. Three-dimensional model of … …Current Research in Bioinformatics, Vol. 5, Issue 1 · 10 Jun 2016 · 8,069 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 and in Vitro Studies: Tryparedoxin Peroxidase Inhibitor Activity of Methotrexate for Antileishmanial ActivityRavi Kumar Gundampati, Shraddha Sahu, Avinash Kumar Srivastava et al.In order to understand the mechanism of molecular interactions at the active site of Tryparedoxin Peroxidase (Try P), homology modeling and docking studies were performed. We generated a Three-Dimensional (3D) model of target protein based on the Crystal structure of Leishmania Major Try PI (PDB ID: 3TUE) using modeler software. Docking analysis was carried out to study the effects of … …American Journal of Infectious Diseases, Vol. 9, Issue 4 · 28 Nov 2013 · 7,893 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, In Vitro and In Vivo Assessment of Safety and Anti-inflammatory Activity of CurcuminM. Venkata, R. Sripathy, D. Anjana et al.Problem statement: Curcumin the active component of turmeric is known for its wide biological actions. Extensive studies on curcumin highlighted its anti-inflammatory, anti-oxidant, anti-microbial, anti-carcinogenic and anti-coagulant activity. The anti-inflammatory activities of curcumin have been demonstrated both in vitro and in vivo. Though curcumin and its anti-inflammatory properties are well documented, the exact mechanism of action and effective in vivo … …American Journal of Infectious Diseases, Vol. 8, Issue 1 · 23 Feb 2012 · 8,999 accessesView PDFCite