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  • Grid-convert
    GRID-CONVERT AUTHOR: Kaushik Raha, John J. Irwin (Derived from Todd Ewing's GRID Program)
    485 bytes (65 words) - 01:02, 11 March 2014
  • Grid Based Score
    ...s based on the non-bonded terms of the molecular mechanic force field (see Grid for more background). Grid Score Parameters
    1 KB (189 words) - 17:28, 15 February 2014
  • OGS/GE
    ...gly refer to this as "SGE", but that is the name of an older product - Sun Grid Engine - that we no longer use.
    664 bytes (107 words) - 16:51, 3 June 2015
  • Contact Score
    ...ce (see Grid). Atom VDW overlaps are penalized by checking the bump filter grid, or with the contact_clash_overlap parameter for the intramolecular score. o contact_score_grid_prefix [grid] (string):
    2 KB (235 words) - 18:10, 8 October 2012
  • Docktools
    ...ation. Docktools consists of chemgrid, solvmap, solvgrid, grid-convert and grid-convrds. This section will briefly review the theory behind each of the pr
    732 bytes (106 words) - 20:11, 8 October 2012
  • Using MakeDOCK
    #REDIRECT [[Understanding MakeDOCK, which automates sphere and grid generation]]
    80 bytes (9 words) - 20:33, 8 October 2012
  • Visualize docking grids
    1.1) The VDW grid 1.2) The electrostatics grid
    861 bytes (138 words) - 23:11, 9 March 2018
  • DOCK 3.7 with GIST tutorials
    * [[Tutorial on running Molecular Dynamics for GIST grid generation]] * [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]]
    437 bytes (61 words) - 19:56, 15 November 2017
  • Bump Filter
    ...amount of atom VDW overlap is defined with the bump_overlap parameter (see Grid). At the time of bump evaluation the number of allowed bumps is defined wit * bump_grid_prefix [grid] (string):
    1 KB (210 words) - 18:10, 8 October 2012
  • Flexible docking code
    the grid generation scripts all start with do_*.csh, i.e. do_chemgrid.csh the other grid generation.
    635 bytes (110 words) - 03:39, 14 February 2014
  • Solvmap
    ...ed high dielectric volume displaced by the protein that is stored for each grid element in the active site. Thus the volume based ligand desolvation energy ...nd complete exposure to the solvent on the protein surface. However, being grid-based it is fast and can be used during conformational search and final sco
    2 KB (274 words) - 04:25, 14 February 2014
  • DOCK Accessories
    ...gand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref>. The program [[grid]] ....1002/jcc.540130412 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (19
    2 KB (229 words) - 22:43, 10 January 2019
  • OpenSGE
    We use one of several OpenSGEs - open versions of sun grid engine, as a queuing system.
    178 bytes (28 words) - 18:11, 22 September 2014
  • Nchemgrids
    0.4 ; grid spacing in angstroms output_prefix ; output grid prefix name
    3 KB (436 words) - 17:44, 15 February 2014
  • Continuous Score
    ...ontinuous scoring is requested, then score parameters normally supplied to grid, must also be supplied to DOCK. It is left to the user to make sure consist #Flag to perform continuous non-grid based scoring as the primary
    3 KB (343 words) - 18:46, 15 February 2014
  • Blastermaster files
    * ligand.desolv.heavy - ligand desolvation scoring grid, non-H atoms * ligand.desolv.hydrogen - ligand desolvation scoring grid, H atoms
    2 KB (294 words) - 15:10, 25 March 2014
  • DOCK 3.5 Score
    DOCK3.5 score is a variant of Grid-based scoring (see Grid). DOCK3.5 score function calculates ligand desolvation in addition to steri #Calculate electrostatic interaction from ESP grid calculated using DelPhi
    3 KB (337 words) - 20:02, 8 October 2012
  • Solvgrid
    ...ligand atom. For the receptor, these can be precalculated and stored on a grid. øDES,BULK(xi) and øDES,EXPL(xi) are interpolated from grids calculated ...vely. Bulk and explicit desolvation grids are calculated from fj and Sj at grid points p, distance rjp from the receptor atom multiplied by gaussian weight
    3 KB (471 words) - 22:33, 12 March 2014
  • Chemgrid
    ...stored on grids. The calculations are based on the theory presented in the Grid section above. However only the steric interaction energy grids are used in 0.33 ; grid spacing in angstroms
    3 KB (365 words) - 05:24, 13 March 2014
  • Ligand desolvation
    ...ed high dielectric volume displaced by the protein that is stored for each grid element in the active site. This calculated by the program solvmap distribu #Bounding box for the grid
    1 KB (227 words) - 05:34, 14 February 2014
  • DOCK Blaster:Job Management
    * Grid preparation submitted * Grid preparation running
    3 KB (449 words) - 20:02, 8 October 2012
  • Zou-GBA Score
    ...processes. It has been tested to obtain similar results compared with the grid-based free energy model but with much less computation efforts. o gbsa_zou_vdw_grid_prefix [grid] (string):
    2 KB (242 words) - 20:33, 8 October 2012
  • Delphi electrostatics
    ...raction energy between the ligand and the receptor is calculated from this grid. For more information please see the [http://dock.compbio.ucsf.edu/DOCK_6/d To create a DelPhi electrostatic grid (phimap) you will need:
    2 KB (248 words) - 04:20, 13 March 2014
  • Other docking servers
    * Design of a grid service based platform for in silico protein-ligand screenings. Levesque
    618 bytes (75 words) - 20:31, 8 October 2012
  • Grid
    USAGE: grid -i grid.in [-stv] [-o grid.out] - i input_file #Input parameters extracted from input_file, or grid.in if not specified
    10 KB (1,588 words) - 20:25, 8 October 2012
  • No viable poses
    specify the margin to perform grid generation ...ritten out in the OUTDOCK file, DOCK will use the intersections of all the grid boxes.
    2 KB (293 words) - 18:05, 25 November 2017
  • OUTDOCK 3.7
    Desolvation grid: ../dockfiles/ligand.desolv.heavy Additional hydrogen desolvation grid: ../dockfiles/ligand.desolv.hydrogen
    3 KB (392 words) - 04:33, 25 February 2014
  • How to protonate a receptor for docking?
    ...ds at all, although you have to option of using the grids generated by the GRID accessory to calculate the vdw term.
    746 bytes (128 words) - 18:15, 2 May 2024
  • Understanding MakeDOCK, which automates sphere and grid generation
    * MakeDOCK automates the process of sphere and grid generation for a target. * Automatically displays non-fatal WARNINGS that occurred during grid generation, which often lead to incorrect docking results.
    3 KB (488 words) - 02:43, 13 March 2014
  • Travel Depth
    (if you want a finer grid size you can specify it after the pdb file, the default is 1 angstrom/grid)
    4 KB (746 words) - 20:33, 8 October 2012
  • Docking tools
    * [[Understanding MakeDOCK, which automates sphere and grid generation]]
    993 bytes (133 words) - 20:11, 8 October 2012
  • PBSA Score
    ...ctric regions and a description of an ion-accessible volume and produces a grid of electrostatic potentials. From this, transfer energies between different *** pbsa_vdw_grid_prefix [grid] (string):
    4 KB (513 words) - 04:01, 14 February 2014
  • DOCK Blaster:1157
    ...ar as the "sampling" I am not sure what this means, but I assume it is the grid size. In any case, it seemed that in the 2.B. set there was a greater diver
    835 bytes (154 words) - 20:02, 8 October 2012
  • Output
    Grid Score: -29.223606
    1 KB (168 words) - 04:01, 14 February 2014
  • Showbox
    ...the location and size of the grids that will be calculated by the program grid , using any graphics program that can display PDB format. The user is asked
    1 KB (180 words) - 22:32, 12 March 2014
  • Flexible Docking: tarting and thin spheres
    Run blastermaster for flexible grid generation: xtal-lig.pdb (--xdist) 5) Grid IDs (--flexgrids) 6) Ground state grid
    6 KB (811 words) - 02:14, 31 December 2020
  • Vdw.defn
    ...W well-depth values are used in molecular mechanics-scoring functions (see Grid). The valence is the value for the maximum number of atoms that can be atta
    2 KB (182 words) - 17:49, 15 February 2014
  • DOCK Overview
    ...heres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations (Kuntz, et al. J. Mol. Biol. 1982 and Shoi ...these sphere centers. Or, a grid may be generated within the site and each grid point may be considered as a sphere center. Our sphere centers, however, at
    10 KB (1,660 words) - 18:50, 15 February 2014
  • DOCK 3.7 tart
    - '''box''' (we use this to trim down the electrostatics grid to the size of the van der Waals and ligand desolvation grids) Next, copy your new "trim.electrostatics.phi" grid into your "dockfiles/" folder. Make sure that your INDOCK file has the corr
    4 KB (579 words) - 18:04, 6 June 2018
  • What does DOCK do?
    centers. Or, a grid may be generated within the site and each grid grids in order to minimize the overall computational time. At each grid
    10 KB (1,568 words) - 23:34, 10 January 2019
  • DOCK3.7 INDOCK
    chemgrid_file ../dockfiles/vdw.vdw #vdw grid file, contains vdw scores delphi_nsize 47 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memor
    5 KB (537 words) - 18:10, 15 February 2014
  • Calculate volume of the binding site and molecules
    *First, Lay a grid over the spheres. *Count the number of points in the grid box (Ng).
    6 KB (873 words) - 18:51, 6 February 2019
  • Blastermaster CLI
    --vdw=VDWPREFIX vdw grid output filename prefix (default: vdw) qnifft grid size (default: 193)
    10 KB (815 words) - 16:09, 25 March 2014
  • SGE Cluster Docking
    *'sgehead.compbio.ucsf.edu' is the submit machine for the Sun Grid Engine (SGE) cluster. wilco is also authorized to submit jobs.
    2 KB (256 words) - 21:36, 27 February 2014
  • INDOCK 3.7
    chemgrid_file ../dockfiles/vdw.vdw #vdw grid file, contains vdw scores delphi_nsize 193 #size of electrostatics grid (cubic). blastermaster.py trims to the minimum size necessary to save memor
    5 KB (622 words) - 23:49, 10 November 2017
  • DOCK 3.5
    ...rid, DISTMAP generated contact grid, and a DelPhi generated electrostatics grid of dimensions 65×65×65. Re-implementing CHEMGRID electrostatics should b
    6 KB (967 words) - 21:44, 10 January 2019
  • Blastermaster
    --vdw=VDWPREFIX vdw grid output filename prefix (default: vdw) qnifft grid size (default: 193)
    10 KB (895 words) - 16:09, 25 March 2014
  • DUMM6
    *precalculate various grid terms
    2 KB (270 words) - 20:11, 8 October 2012
  • FEP+ for GPCR
    ...d for docking from the .mae file you generated above using the '''Receptor Grid Generation''' tool.
    5 KB (754 words) - 19:55, 8 February 2024
  • How to cite
    Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (19
    2 KB (231 words) - 21:50, 6 December 2018
  • INDOCK for DOCK 3.6
    ...There are 2 ways to run 'volume' or partial desolvation, one is to use one grid for every ligand atom like this: The other option is to use one grid for ligand heavy atoms and one for ligand hydrogen atoms, you'll want to un
    11 KB (1,394 words) - 18:09, 15 February 2014
  • ZINC22 Partitions
    ...y adjacent, such that each one forms a square or rectangle on the tranche "grid".
    3 KB (479 words) - 04:27, 25 December 2020
  • History of DOCK 6
    molecular mechanics interaction energies using grid files calculated by CHEMGRID (which is now superseded by GRID in version 4.0). More
    6 KB (893 words) - 15:26, 5 April 2016
  • DOCK:History
    ...ergies using grid files calculated by CHEMGRID (which is now superseded by GRID in version 4.0). More information about the ligand and receptor molecules i * electostatic scoring grid computed with [[Delphi]].
    11 KB (1,545 words) - 17:01, 27 January 2021
  • Loading And Creating ZINC Partitions Automatically
    ...fine tranches themselves. Specifically, we need a "heatmap", which is a 2D grid of values representing the number of molecules in each fine tranche bucket.
    3 KB (499 words) - 04:07, 29 May 2020
  • Classic Dock References
    ...rman P.F.; Hodge C.N.; Zacharias M.; McCammon J.A. A Molecular Mechanics / Grid Method for Evaluation of Ligand-Receptor Interactions. J. Comput. Chem. 16: Meng, E.C., Shoichet, B.K. and Kuntz, I.D. Automated docking with grid-based energy evaluation. J. Comp. Chem. 13: 505-524, 1992.
    5 KB (736 words) - 23:22, 11 March 2014
  • DOCK 3.8
    ...pt)|Running pydock3/blastermaster (classic blastermaster script - generate grid files)]]
    3 KB (413 words) - 17:06, 8 April 2023
  • Protein Target Preparation Updated
    ...e, by solving the Poisson-Boltzmann equation using the program QNIFFT. The grid is trimmed to fit the DOCK box (called "box" in the working directory), whi ligand.desolv.heavy ### grid you want to generate
    16 KB (2,467 words) - 18:59, 10 October 2019
  • Lab Virtual Machines
    gamma Sun Grid Engine
    4 KB (597 words) - 17:29, 21 August 2018
  • Hawkins GB/SA Score
    #calculated continuously or from a grid
    4 KB (526 words) - 05:11, 14 February 2014
  • Membrane Modeling
    ...is generated around the target receptor and included in the docking score grid generation. ...g coarse-grained system to atomistic resolution and select lipid atoms for grid generation =
    23 KB (3,565 words) - 21:36, 31 May 2023
  • Install operating system
    We recommend free versions of Sun Grid Engine [[SGE]].
    3 KB (532 words) - 18:32, 22 September 2014
  • Cluster 2
    * gamma - sun grid engine qmaster
    4 KB (587 words) - 00:43, 8 January 2019
  • DOCK 3.6 User Manual
    * Receptor grid (generated with delphi)
    7 KB (721 words) - 22:17, 2 January 2019
  • MPose
    ...de>INDOCK</code> file inside. It will also resolve the file paths (such as grid files and database file) mentioned in <code>INDOCK</code>, and make sure th
    6 KB (983 words) - 05:12, 14 February 2014
  • Analysing the results
    *enter the name of the grid for partial desolvation, presumably <tt>grids/solvmap</tt> or <tt>grids/sol
    5 KB (949 words) - 18:10, 8 October 2012
  • Sun Grid Engine (SGE)
    ALL ABOUT SGE (SUN GRID ENGINE) # when the value is empty or path does not exit on the system, Grid Engine
    25 KB (3,771 words) - 20:56, 23 January 2017
  • Dockenv Scripts
    grids - templates for grid directory. instantiated by Makefile
    5 KB (845 words) - 17:25, 2 May 2024
  • TLDR
    * workfiles, which may be used for grid and sphere optimization.
    6 KB (941 words) - 20:27, 29 April 2024
  • Installing DOCK 6
    Conformations and different Contact or Grid scores.
    8 KB (1,195 words) - 19:52, 10 January 2019
  • Ligand Flexibility
    Lyr:5 Seg:0 104/882 retained, Pruning: 15-outside grid 22-score 741-clustered t=77.71s ...46-21) or 225 conformers were pruned: 2 conformers were outside the energy grid, 5 conformers exceeded the score cut-off (see ''pruning_conformer_score_cut
    18 KB (2,718 words) - 23:58, 23 March 2016
  • Tutorial on running Molecular Dynamics for GIST grid generation
    Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodyn get center of grid from aligned.lig.pdb
    26 KB (4,023 words) - 00:21, 5 March 2019
  • SGE notes
    ALL ABOUT SGE (SUN GRID ENGINE)
    13 KB (1,923 words) - 22:02, 16 May 2016
  • SUBDOCK DOCK3.8
    # SGE (Sun Grid Engine)
    12 KB (1,896 words) - 02:59, 28 December 2023
  • Tutorial on running DOCK3.7 with GIST
    ...ompleted the MD tutorial [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts]].
    18 KB (2,525 words) - 01:31, 16 November 2017
  • GPU DOCK
    ...contains a CUDA/C++ side data structure for the phimap (the electrostatics grid).
    20 KB (3,437 words) - 20:50, 22 April 2023
  • Tutorial on running Molecular Dynamics for GIST grid generation with scripts
    Grid inhomogeneous Solvation Theory (GIST) is a method for calculating thermodyn ...in without any cofactors [[Tutorial on running Molecular Dynamics for GIST grid generation with scripts 2]].
    49 KB (7,168 words) - 00:18, 9 November 2017
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