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23 articles for “Molecular Modeling”
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Research ArticleOpen accessPhrase in the titleThe Development of New Molecules Having Antiemetic Activity Using Molecular ModelingKhalil Errahmane Kanouni, Yacine BenguerbaThe solubility of a drug in water or in the blood represents the most desired parameter in medicine. Our aim is to obtain molecules with properties more effective than those of metoclopramide. In this work, two molecules with high solubility are constructed. Metoclopramide (a benzamide derivative) is a dopamine receptor antagonist used as an antiemetic drug. Its solubility in water … …Current Research in Bioinformatics, Vol. 8, Issue 1 · 27 Feb 2020 · 6,664 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleHOMOLOGY MODELING AND MOLECULAR DYNAMICS STUDIES OF EC1 DOMAIN OF VE-CADHERIN TO ELUCIDATE DOCKING INTERACTION WITH CADHERIN-DERIVED PEPTIDEVivitri Dewi Prasasty, Usman Sumo Friend Tambunan, Teruna Jaya SiahaanVE-cadherin is a protein in the cadherin family that is found at the adherens junctions of the microvessel endothelial cells of the Blood-Brain Barrier (BBB). It is recognized as the homotypic cell adhesion molecules and there is limited structural information on how VE-cadherins mediate cell-cell adhesion. It has been shown that the EC1 domain of cadherins is important for the … …OnLine Journal of Biological Sciences, Vol. 14, Issue 2 · 25 Jun 2014 · 7,530 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleUPLC-Q-Exactive Orbitrap-MS Analysis of Anchusa italica Retz. Flowers: Molecular Docking, Dynamics Modeling, and Pharmacokinetics for Cardiovascular DiseaseLinyang Wang, Yan Chen, Ainiwaer Aikemu, Shuge TianThis study builds on prior UPLC-Q-Exactive Orbit rap-MS analyses of Anchusa italica Retz. Flowers (Airfs) to explore their anti-cardiovascular mechanis·ms and key bioactive markers. UPLC-Q-Exactive Orbitrap-MS identified 30 major compounds, including polyphenols and flavonoids with strong antioxidant activity. The potential active ingredients were then screened using Lipinski's rule of five, and a network pharmacology method was employed to construct an … …American Journal of Biochemistry and Biotechnology, Vol. 21, Issue 2 · 25 Oct 2025 · 2,599 accessesView PDFCite
Research ArticleOpen accessEvery word in the titleModeling 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 PDFCite
Research ArticleOpen accessIn the keywordsProbing the Substrate Specificity and Intersubunit Interactions of Brevundimonas Diminuta Glutaryl Acylase with Site-Directed MutagenesisMichael Eldarov, Anna Lyashenko, Tatyana Sherbakova et al.Glutaryl-7-ACA acylases (GLA) are industrial enzymes widely used for the production of 7-aminocepahlosporanic acid (7-ACA)-the starting compound for manufacturing of semisynthetic cephalosporin antibiotics. Generation of mutant GLA's with increased activity and stability, capability for single-step conversion of cephalosporin C (CPC) directly to 7-ACA is a promising route to improve the current biocatalytic technologies. In this study GLA from Brevundimonas diminuta … …American Journal of Biochemistry and Biotechnology, Vol. 10, Issue 3 · 12 Nov 2014 · 8,160 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 keywordsMolecular Docking of New Active Compounds Towards the Acetylcholinesterase EnzymeLemaoui Tarek, Hammoudi Nour El Houda, Benguerba Yacine, Attoui AyoubMolecular docking is a key instrument in structural molecular biology and computer-assisted drug design. The objective of ligand-protein docking is to expect the main binding mode(s) of a ligand with a protein of known three-dimensional structure. Effective docking methods search high-dimensional spaces effectively and finding a scoring function that correctly ranks candidate dockings (Morris et al., 2008). In this study … …Current Research in Bioinformatics, Vol. 8, Issue 1 · 27 Feb 2020 · 11,404 accessesView PDFCite
Research ArticleOpen accessIn the keywordsStructural Consequences of the Polymorphism Q223R in the Human Leptin Receptor: A Molecular Dynamics StudyJonathan P. Carrillo-Vázquez, Brenda Chimal-Vega, Beatriz Zamora-López et al.Leptin Receptor (LEPR) is a component of a signaling pathway related to appetite and energy expenditure. Single Nucleotide Polymorphisms (SNP) of Leptin receptor gene (lepr) have been proposed as possible modulator of adipose tissue and body weight. The main phenomenological consequence reported of these SNPs is the modulation of the LEP-LEPR interaction promoting the weight gain. Particularly, Q223R polymorphism has … …American Journal of Agricultural and Biological Sciences, Vol. 8, Issue 3 · 23 Sep 2013 · 7,835 accessesView PDFCite
Research ArticleOpen accessIn the keywordsProtein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A ReviewPeiqiang YuThe utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of … …American Journal of Biochemistry and Biotechnology, Vol. 3, Issue 2 · 30 Jun 2007 · 8,286 accessesView PDFCite
Research ArticleOpen accessIn the abstractEffects of Aerobic Exercise on PPAR-γ Expression in Adipose Tissue and RT-PCR Detection AnalysisXiaodong Zhan, Chenguang Bi, Jie WeiThis study aimed to examine the effect of organized aerobic exercise on the expression level of Peroxisome Proliferator-Activated Receptor gamma (PPAR-γ) gene in adipose tissue by performing digital variant of RT-PCR, Droplet Digital PCR (ddPCR) which is a highly sensitive method for counting the gene copy numbers. The proposed scheme consists of three-stage analytical procedure, namely, Subphase I Controlled Aerobic … …American Journal of Biochemistry and Biotechnology, Vol. 22, Issue 3 · 29 Sep 2026 · 580 accessesView PDFCite