24 articles for “Docking Interaction”

Research ArticleOpen accessIn the abstractStructural 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 PDF Cite

Research ArticleOpen accessIn the abstractAqueous Extracts of Bay Leaf (Laurus nobilis) and Rosemary (Rosmarinus officinalis) Inhibit Iron-Induced Lipid Peroxidation and Key-Enzymes Implicated in Alzheimer’s Disease in Rat Brain-in VitroAyodeji O. Falade, Goodness I. Omolaiye, Kayode E. Adewole et al.Neurological disorders remain a global health challenge, with Alzheimer’s Disease (AD) as the most famous cause of dementia in old people. Nevertheless, culinary spices and herbs have shown promising potentials in the management of neurological diseases. This study aimed at investigating the neuroprotective property of aqueous extracts of bay leaf (Laurus nobilis) and rosemary (Rosmarinus officinalis) by assessing the antioxidant … …American Journal of Biochemistry and Biotechnology, Vol. 18, Issue 1 · 25 Jan 2022 · 7,955 accessesView PDF Cite

Research ArticleOpen accessIn the abstractIn 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 PDF Cite

Research ArticleOpen accessIn the abstractStatistical Improvement of Batch Culture with Immobilized Pichia pastoris Cells for rPOXA 1B Laccase ProductionMichelle Gouzy-Olmos, Luis M. Cháves-Tequia, María F. Rojas-Fajardo et al.Immobilized Pichia pastoris X33/pGAPZαA-LaccPost-Stop in Ca2+ alginate beads was employed for Pleurotus ostreatus rPOXA 1B laccase batch production. Sequential statistical improvement was achieved through Plackett-Burman (PBED), (PBED-T11, 29.5±0.8 UL-1), which allowed to increase activity by 2.36-fold (12.5±2.6 UL-1) obtained in a preliminary study. Following, Box-Behnken Experimental Design (BBED) was implemented and obtained enzymatic activity in PBED-T11 was further increased by … …American Journal of Biochemistry and Biotechnology, Vol. 14, Issue 2 · 26 Apr 2018 · 11,776 accessesView PDF Cite

Research ArticleOpen accessIn the abstractDesigning 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 PDF Cite

Research ArticleOpen accessIn the abstractStructure 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 PDF Cite

Research ArticleOpen accessIn the abstractIn 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 PDF Cite

Research ArticleOpen accessIn the abstractModeling and Molecular Docking Studies on Rnase Aspergillus niger and Leishmania donovani Actin: Antileishmanial ActivityRavi Kumar Gundampati, Shraddha Sahu, Kirti Shila Sonkar et al.A.niger Rnase was designed from ACTBIND (PDB ID: 3D3Z). Yeast actin-human gelsolin segment 1 complex (PDB ID: 1YAG) was used as template for L. donovani actin protein for 3D model in Modeller9v8. These models were testified by PROCHECK, ERRAT, WHAT-IF, PROSA2003 and VERIFY-3D. All evidences suggest that the geometric quality of the backbone conformation, energy profile, residue interaction and contact … …American Journal of Biochemistry and Biotechnology, Vol. 9, Issue 3 · 21 Sep 2013 · 7,527 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 abstractIN 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 PDF Cite