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  • Open Source Software
    * datawarrior - chemoinformatics visualization and data analysis
    199 bytes (23 words) - 20:52, 5 June 2017
  • Visualizing delphi
    # go to the visualization tab [[Image:Visualization.png|thumb|none]]
    1 KB (236 words) - 18:50, 15 February 2014
  • Adding Static Waters to the Protein Structure
    ...DOCK3.7 can use them, but you have to add hydrogens 'manually' using some visualization program and your intuition.
    931 bytes (119 words) - 19:02, 12 April 2019
  • Visualize docking grids
    [[Category:Visualization]]
    909 bytes (142 words) - 00:26, 25 May 2024
  • Showbox
    Showbox is an interactive program that allows visualization of the location and size of the grids that will be calculated by the progra
    1 KB (180 words) - 22:32, 12 March 2014
  • Hackathon 2024 to consolidate the standard lab protocol
    * grid visualization protocols
    1 KB (216 words) - 00:33, 25 May 2024
  • Chimera Tutorial (Delta opioid receptor)
    [[Category:Visualization]]
    1 KB (181 words) - 18:06, 2 May 2024
  • Minimize protein-ligand complex with AMBER
    You can do this in a number of ways. You can use your favorite molecular visualization software like UCSF Chimera. Or, you can use your favorite text editor like == Step 5. Convert to pdb for easy visualization. ==
    7 KB (1,147 words) - 01:34, 15 December 2018
  • Interactive ligands visualizer
    ...hat file (see below), and then a generated script will show an interactive visualization of the chemical space spanned by the ligands (tSNE), with each molecule sho '''Step 5: tSNE and interactive visualization'''
    5 KB (855 words) - 23:54, 27 January 2023
  • Contributed Code
    ...phere_select can also automatically write out the sphere PDB file for easy visualization.
    3 KB (491 words) - 14:05, 15 February 2014
  • Irwin:workshop1
    ...yMOL], [http://www.cgl.ucsf.edu/chimera Chimera] or any other 3D molecular visualization tool for looking at the docking hits. The website for SEA is [http://sea.do
    4 KB (578 words) - 20:27, 8 October 2012
  • DOCK 3.7 2014/09/25 FXa Tutorial
    === pose visualization ===
    9 KB (1,429 words) - 23:37, 26 April 2016
  • Ligand File Input
    or various other visualization packages. During the docking procedure,
    4 KB (576 words) - 23:28, 23 March 2016
  • Ligand File I/O
    ...file for the ligand (see Structure Preparation Tutorial) or various other visualization packages. During the docking procedure, ligands are read in from a single M
    5 KB (693 words) - 17:44, 2 May 2024
  • Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2
    # for ease of visualization in pymol
    5 KB (793 words) - 16:26, 3 May 2017
  • Oracle scraps
    ...results as first 100 returned for page, then can continue searching while visualization calls present the webpage)
    5 KB (681 words) - 17:01, 18 March 2014
  • Calculate volume of the binding site and molecules
    * Select the cluster that defines the binding site of interest by visualization in Chimera.
    6 KB (873 words) - 18:51, 6 February 2019
  • Coloring and Subcluster Matching
    The script generates two matching sphere files: matching_spheres.vis.sph for visualization in Chimera: spheres with different chemical features such as hbond acceptor
    8 KB (878 words) - 20:37, 12 April 2022
  • Ligand Flexibility
    ...own ligand, including minimizations. This newly implemented feature allows visualization of all stages of growth and optimize behavior of current DOCK routines. Not
    18 KB (2,718 words) - 23:58, 23 March 2016
  • Tutorial on running Molecular Dynamics for GIST grid generation with scripts
    # for ease of visualization in pymol ## parameters to add if writing NetCDF -- for production run not visualization (VMD)
    49 KB (7,168 words) - 00:18, 9 November 2017
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