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• Ligand desolvation
  ...olvation. Volume based desolvation is calculated by multiplying the atomic desolvation by a normalization factor that accounts for the burial of the ligand atom i
  1 KB (231 words) - 00:23, 25 May 2024

Page text matches

• Ligand desolvation
  ...olvation. Volume based desolvation is calculated by multiplying the atomic desolvation by a normalization factor that accounts for the burial of the ligand atom i
  1 KB (231 words) - 00:23, 25 May 2024
• What's new in DOCK 6.0
  ...s, ligand conformational entropy corrections, ligand desolvation, receptor desolvation; Hawkins-Cramer-Truhlar GB/SA solvation scoring with optional salt screenin
  542 bytes (60 words) - 18:47, 15 February 2014
• Solvmap
  ...red for each grid element in the active site. Thus the volume based ligand desolvation energy is calculated as: Here L is the ligand atom desolvation, volume summed over k volume elements, V. This method is only an approximat
  2 KB (278 words) - 00:26, 25 May 2024
• Removing Spheres (The Chase Method)
  ...nd desolvation spheres around atom(s) of interest. This is to decrease the desolvation cost in a targeted way. ...e. It requires the coordinates of the atoms that you want to remove ligand desolvation spheres from. The default distance of removing of these spheres is 3 Å.
  2 KB (386 words) - 20:17, 27 May 2020
• 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
• Docktools
  ...includes different grid-based methods for calculating ligand and receptor desolvation. Docktools consists of chemgrid, solvmap, solvgrid, grid-convert and grid-c
  732 bytes (106 words) - 20:11, 8 October 2012
• Solvgrid
  ...nature where desolvation energy can be described pairwise additively. The desolvation energy due to interaction between a ligand atom and receptor atom can be ca ...the fragmental volume of the receptor atom respectively. Bulk and explicit desolvation grids are calculated from fj and Sj at grid points p, distance rjp from the
  3 KB (475 words) - 00:26, 25 May 2024
• DOCK 3.5 Score
  ...of Grid-based scoring (see Grid). DOCK3.5 score function calculates ligand desolvation in addition to steric and electrostatic interactions between the ligand and #Calculate total or volume based ligand desolvation from solvation
  3 KB (337 words) - 20:02, 8 October 2012
• DOCK 3.6
  ..., as described in Mysinger MM, Shoichet BK, Rapid context-dependent ligand desolvation in molecular docking, J Chem Inf Model. 2010 Sep 27;50(9):1561-73 = Ligand Desolvation =
  2 KB (326 words) - 22:15, 2 January 2019
• OUTDOCK 3.7
  Solvation type: context-dependent ligand desolvation Ligand desolvation treatment. Choices are None, Full, and Context-dependent
  3 KB (392 words) - 04:33, 25 February 2014
• Methods section
  ...ional ensembles (omega v2.5.1.4, www.eyesopen.com)51, atomic charges52 and desolvation energies53,54 are calculated as described55. ...Omega100 (OpenEye Scientific Software, Santa Fe NM).101 Atomic charges and desolvation penalties are calculated using AMSOL 7.1102 and our previously published pr
  2 KB (328 words) - 21:37, 7 April 2022
• Analysing the results
  Or for custom grids, used below to run SEV-based desolvation grids ===Atomic contributions to the desolvation===
  5 KB (949 words) - 18:10, 8 October 2012
• DOCK:Problems
  * treatment of receptor desolvation
  611 bytes (76 words) - 20:02, 8 October 2012
• Blastermaster CLI
  ligand desolvation output filename (default: ligand desolvation program (default: /raid4/people/tsk
  10 KB (815 words) - 16:09, 25 March 2014
• How to do parameter scanning
  ..., updated 12/2019 so users can specify different low dielectric and ligand desolvation sphere radii To generate different sized low dielectric and ligand desolvation thin sphere combinations, you must first run blastermaster on your protein/
  6 KB (819 words) - 15:35, 2 August 2024
• Blastermaster
  ligand desolvation output filename (default: ligand desolvation program (default: /raid4/people/mat
  10 KB (895 words) - 16:09, 25 March 2014
• Dock Sampling
  ...mations and the partial charges generated by Amsol (and therefore also the desolvation energies) will also be changed. <br> ===3. Optional: calculate electrostatics, vdw and desolvation for a DOCK orientation ===
  8 KB (1,222 words) - 16:11, 14 February 2014
• Visualize docking grids
  1.3) The desolvation grid
  909 bytes (142 words) - 00:26, 25 May 2024
• Analyzing DOCK Results
  psol is the ligand polar desolvation asol is the ligand apolar desolvation
  3 KB (580 words) - 14:34, 30 March 2020
• Analyzing DOCK 3.7 Results
  psol is the ligand polar desolvation asol is the ligand apolar desolvation
  3 KB (601 words) - 21:22, 13 February 2014