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39 results for “Molecular docking”
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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 keywordsMolecular 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 PDFCite
Research ArticleOpen accessIn the keywordsIn silico Modeling of α1A-Adrenoceptor: Interaction of its Normal and Mutated Active Sites with Noradrenaline as well as its Agonist and AntagonistRamchandran Vijayan, Naidu Subbarao, Birendra Nath MallickNoradrenaline, like most other neurotransmitters, acts through various adrenoceptor subtypes. The structure and active site of adrenoceptors for the binding of noradrenaline were unknown, however, such information are crucial for understanding the molecular mechanism of action of neurotransmitters, including noradrenaline, in health and disease as well as for drug designing. In this in silico study, we modeled the α1A-adrenoceptor; a … …American Journal of Biochemistry and Biotechnology, Vol. 3, Issue 4 · 31 Dec 2007 · 7,140 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 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 keywordsBioactive Compounds Screening from Zingiberaceae Family as Influenza A/Swine Flu Virus Neuraminidase Inhibitor through Docking ApproachUsman Sumo Friend Tambunan, Fadilah, Arli Aditya ParikesitProblem statement: Influenza A/H1N1 is a disease caused by infection of influenza a virus subtype H1N1. It is a major health problem in tropical and subtropical countries. This virus constantly mutates and consequently will be developed into new drug-resistant strains. Approach: In this research, we have conducted docking study to screen bioactive compounds from Zingiberaceae family, which has a role … …OnLine Journal of Biological Sciences, Vol. 10, Issue 4 · 31 Dec 2010 · 8,616 accessesView PDFCite
Research ArticleOpen accessIn the abstractComputational Validation of Selected Compounds from the GC-MS Profile of Abies numidica Essential Oil and their Antibacterial EffectsAbdelouahab Dehimat, Boudjellal Fayssal, Salem Dounya et al.This work examined the chemical composition of the Algerian endemic tree Abies numidica (Pinaceae) and investigated the antibacterial potential of three major constituents of its essential oil-Santene, Linalyl acetate, and 2,6-Octadiene-2,6-dimethyl-as reported in previously published GC-MS data. Computational antibacterial screening was carried out by docking the selected compounds onto the bacterial proteins 5Z9N (Staphylococcus aureus) and 3AQC (Micrococcus luteus). Molecular … …Current Research in Bioinformatics, Vol. 10, Issue 1 · 24 Jan 2026 · 2,939 accessesView PDFCite
Research ArticleOpen accessIn the abstractThe Effect of NaCl on the Stability of Ab3 Lipase from Sphingobacterium sp. that Co-Expressed with LEA K Using In silico ApproachIbrahim Muhammad et al.This study explores how sodium chloride (NaCl) influences the binding affinity and stability of the Ab3 lipase-LEA K complex when interacting with olive oil, using molecular docking techniques. The docking simulations, conducted with AutoDock Vina, reveal that the presence of NaCl significantly enhances the binding affinity of the enzyme-substrate complex, increasing it from-6.55 kcal/mol in the absence of salt to-7.81 … …American Journal of Biochemistry and Biotechnology, Vol. 21, Issue 1 · 9 Mar 2025 · 5,599 accessesView PDFCite
Research ArticleOpen accessIn the abstractEnhancement of Geobacillus thermodenitrificans Lipase Activity and Binding Affinity by Acetone Treatment: Kinetic and in silico InvestigationsAmmar Khazaal Kadhim Almansoori, Alyaa Abdulhussein Alsaedi et al.Lipase Geobacillus thermodenitrificans (LipGt) is a thermostable enzyme that has an optimal activity temperature of 65°C. It can tolerate various organic solvents and has an improved activity, especially in the presence of acetone. In this study, in-vitro and in-silico studies were carried out to investigate the effect of acetone in enhancing the kinetic and binding affinity of LipGt. The LipGt … …American Journal of Biochemistry and Biotechnology, Vol. 20, Issue 4 · 10 Oct 2024 · 4,817 accessesView PDFCite