DOCK Accessories: Difference between revisions

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the sphere centers that fill the site. It has been described in the
the sphere centers that fill the site. It has been described in the
original paper ([[Kuntz et al. J. Mol. Biol. 1982]]). The program [[grid]]
original paper ([[Kuntz et al. J. Mol. Biol. 1982]]). The program [[grid]]
generates the scoring grids
generates the scoring grids <ref name='bks1992' >[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130311 Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992).]</ref><ref>[http://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.540130412 Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).]</ref>. Within the DOCK suite of
([[Shoichet et al. J. Comp. Chem. 1992]] and
[[Meng et al. J. Comp. Chem. 1992]]). Within the DOCK suite of
programs, the program DOCK matches spheres
programs, the program DOCK matches spheres
(generated by [[sphgen]]) with ligand atoms and uses
(generated by [[sphgen]]) with ligand atoms and uses
scoring grids (from [[grid)]] to
scoring grids (from [[grid)]] to
evaluate ligand orientations ([[Kuntz et al. J. Mol. Biol. 1982]] and
evaluate ligand orientations <ref>[http://www.sciencedirect.com/science/article/pii/002228368290153X?via%3Dihub Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)]</ref><ref name='bks1992' />. Program DOCK also minimizes
[[Shoichet et al. J. Comp. Chem. 1992]]). Program DOCK also minimizes
energy based scores.<ref>[https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.340170305 Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)]</ref>
energy based scores ([[Meng et al. Proteins. 1993]]).
 
=References=
<references />

Revision as of 22:39, 10 January 2019

The relationship between the main programs in the dock suite is depicted in Figure 1. These routines will be described below.

< insert dock6_manual_files/dock_workflow.JPG >

Main programs in DOCK suite

The program sphgen identifies the active site, and other sites of interest, and generates the sphere centers that fill the site. It has been described in the original paper (Kuntz et al. J. Mol. Biol. 1982). The program grid generates the scoring grids [1][2]. Within the DOCK suite of programs, the program DOCK matches spheres (generated by sphgen) with ligand atoms and uses scoring grids (from grid) to evaluate ligand orientations [3][1]. Program DOCK also minimizes energy based scores.[4]

References

  1. ↑ 1.0 1.1 Shoichet BK, Bodian DL, Kuntz ID. Molecular docking using shape descriptors. Journal of Computational Chemistry 13, 380-397 (1992).
  2. ↑ Meng EC, Shoichet BK, Kuntz ID. Automated docking with grid-based energy evaluation. Journal of Computational Chemistry 13, 505-524 (1992).
  3. ↑ Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161, 269-288 (1982)
  4. ↑ Meng EC, Gschwend DA, Blaney JM, Kuntz ID. Orientational sampling and rigid‐body minimization in molecular docking. Protein 17, 266-278(1993)
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