in the present study, the antimicrobial tests of patchouli oil were studied by using molecular docking technology and antimicrobial test in vitro. five biological macromolecule enzymes, required by the bacteria in the process of biosynthesis were selected as target molecules. five antibiotics benzylpenicillin, sulfadiazine, trimethoprim, rifampicin and ciprofloxacin, which are generally acknowle...

the antidiuretic effect of arginine vasopressin (avp) is mediated by the vasopressin v2 receptor. the docking study of avp as a ligand to v2 receptor helps in identifying important amino acid residues that might be involved in avp binding for predicting the lowest free energy state of the protein complex. whereas previous researchers were not able to detect the exact site of the ligand-receptor...

background: luxi is a component of the quorum sensing signaling pathway in vibrio fischeri responsible for the inducer synthesis that is essential for bioluminescence. methods: homology modeling of luxi was carried out using phyre2 and refined with the galaxyweb server. five models were generated and evaluated by errat, anolea, qmean6, and procheck. results: five refined models were generated b...

A hybrid docking simulator is a hardware-in-the-loop (HIL) simulator that includes a hardware element within a numerical simulation loop. One of the goals of performing a HIL simulation at the European Proximity Operation Simulator (EPOS) is the verification and validation of the docking phase in an on-orbit servicing mission. A key feature of the HIL docking simulator setup is a feedback loop ...

The Topoisomerase I enzyme has become an attractive target for the treatment of cancer. In this paper molecular dynamics, 2D and 3D QSAR and molecular docking studies were performed on 90 naphthoquinone derivatives as Topoisomerase I inhibitors by using the human Topo I-DNA cleavable complex. This model has the drug intercalated with its planar pharmacophore between +1 and -1 bp flanking cleava...

The ligand-receptor interaction between some peptidomimetic inhibitors and a class II MHC peptide presenting molecule, the HLA-DR4 receptor, was modeled using some three-dimensional (3D) quantitative structure-activity relationship (QSAR) methods such as the Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA), and a pharmacophore building met...

Human immunodeficiency virus infection/acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR inhi...

Decoys As the Reference State (DARS) is a simple and natural approach to the construction of structure-based intermolecular potentials. The idea is generating a large set of docked conformations with good shape complementarity but without accounting for atom types, and using the frequency of interactions extracted from these decoys as the reference state. In principle, the resulting potential i...

Scorpion venom contains different toxins with multiple biological functions. IMe-AGAP is the first Analgesic-Antitumor like Peptide (AGAP) isolated from Iranian scorpion Mesobuthus eupeus. This peptide is similar to AGAP toxin with high analgesic activity, extracted from Chinese scorpion and inhibits NaV1.8 and NaV1.9 voltage-gated sodium channels involved in the ...

BACKGROUND Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come wit...