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Lysophosphatidic acid receptor 6 (LPAR6) is a G-protein coupled receptor (GPCR) involved in hair development and cytoskeleton formation in mammals. Its proliferation is implicated in several forms of cancer including liver cancer, squamous cell carcinoma and metastatic prostate cancer. Current study emphasizes the isolation of competitive non-lipid and stable peptide antagonists for Lysophosphatidic acid ligand. A total of 148 conotoxin structures were characterized for their binding abilities against LPAR6. Subsequently, top 10 conotoxins were selected on the basis of binding energy values, residual contributions and conformational cluster saturations. BuIA (a member of Alpha- conotoxins family), contryphan-R and contryphan-Lo (Synthetic class) conotoxins, exhibiting efficient binding parameters were subjected to molecular dynamics simulation assays and topology analysis. We propose that BuIA might be a potent antagonist due to its predominant binding at the extracellular region of LPAR6. Current study provides a backbone for understanding structural and functional insights of LPAR6 and findings of this study may be helpful in designing novel therapeutic targets for the treatment of cancers caused by elevated LPAR6 expression.
Pubmed ID: 29211777
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Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.
View all literature mentionsCollection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.
View all literature mentionsA vector graphics software which runs on Windows, Mac OS X and GNU/Linux. It can import and export various file formats, including SVG, AI, EPS, PDF, PS and PNG. Features include object creation, object manipulation, color editing, and text editing.
View all literature mentionsPictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.
View all literature mentionsWeb server for the detection of the transmembrane regions of membrane proteins using their 3D structure only.
View all literature mentionsSoftware suite of automated docking tools. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure. AutoDock consist of AutoDock 4 and AutoDock Vina. AutoDock 4 consists of autodock to perform docking of ligand to set of grids describing target protein, and autogrid to pre calculate these grids.
View all literature mentionsA software package created to perform molecular dynamics. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have many complicated bonded interactions, but it can also be used for research on non-biological systems, such as polymers.
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