See 'Modification and Editing of RNA', edited by Henri Grosjean chapter 11. * normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 ( link) See: SmartCYP and SmartCYP - background Patrik Rydberg, David E. The three top-ranked atoms are highlighted. CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. * CYP Metabolic sites predicted with SMARTCyp. * Chemical properties calculated with Open Babel - O'Boyle et al. To follow along you can use the applet at right or download the file and open it in a copy of the Jmol application. HMDB (Human Metabolome Database) no exac match, link to the most similar ligand The display at right is from the file ethane-staggered-3-21G.log. PDB no exac match, link to the most similar ligand Number of Hydrogen Bond Acceptors 2 (HBA2) The following script, for example, might modify the bonding to oxygen. Also how to put Jmol commands in REMARK lines in the headers of PDB or PNGJ files.Number of Hydrogen Bond Acceptors 1 (HBA1) There are two basic Jmol command types - RasMol-like commands (shown in bold. How to put the loaded PDB file into an array of lines, edit those lines with Jmol commands, and write a new PDB file. An energy minimization may be convenient afterwards, or you can use the special minimize addHydrogens command to do both in one go.Īllows to delete all atoms in a certain model/frame. See also section How to change atom coordinates in the mouse manual.Īllows to add atoms and to add or redefine atom-associated properties (such as coordinates, charge, radius, temperature factor, occupancy, vibration, etc., or custom properties).Ĭalculate hydrogens allows to add hydrogen atoms, at reasonable positions, in models that lack them. Reassigns all bonds of aromatic type as alternating single and double aromatic bonds.Ĭalculate structure does not really change bonds, but assignation of secondary structure for proteins and, hence, cartoon/ribbon rendering and coloring by structure.Ĭhanges atom coordinates according to some XYZ values (or fractional crystallographic coordinates).Ĭhanges atom coordinates applying a rotation operation.Ĭhanges atom coordinates applying a symmetry operation.Ĭhanges atom coordinates following a force field calculation in search of a conformation of minimal energy. Makes Jmol calculate a limited set of likely hydrogen bonds. Use the search box to search using the name of a molecule or click on one of the buttons below. It is possible to read the bond lengths and bond angles from the images. It can retrieve structural data on molecules from databases and plot the molecules in three dimensions. Either all multiple bonds are shown or all are not. JSmol molecule viewer JSmolis an open source molecule viewer. Note that there is no selection option here. Defines whether Jmol will add bonds based on interatomic distances (for file formats that do not specify bonds).Īllows to add or delete bonds arbitrarily, or to change bond order. select carbon wireframe off wireframe on Displaying multiple bonds.
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