Search results

...is stored 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 o

...ed into the output. If a parameter is not needed it is not reported in the output. At the completion of each DOCK run, the number of molecules that were proc ...mation Search Tree), and a breakdown of the interaction energy between the ligand and receptor (see Scoring).

...GA). Maybe you are interested to find out if a bioactive conformation of a ligand as represented in a crystal structure is actually generated by OMEGA. ===1. Output OMEGA conformations (generated by dbgen.csh) into mol2 file===

...the PLOP control file to perform more sophisticated analysis. The scoring output format is consistent with that of [[MUD - Michael's Utilities for Docking]] Simply invoke <code>eplop</code> with paths to the receptor and the ligand:

...he docking procedure, ligands are read in from a single MOL2 or multi-MOL2 file. Atom and bond types are assigned using the DOCK 4 atom/bond typing paramet ...cored.mol2. Beyond this option, there are several other levels of sampling output:

...dentified with the chemical_match_file parameter and reside in an editable file (see chem_match.tbl). If a match will produce unfavorable interactions, the

This may take awhile but it will pull all your results into a single file, etc. If you want to calculate enrichment, etc.: $d37/enrich.py -l ligand-file -d decoy-file

This may take awhile but it will pull all your results into a single file, etc. If you want to calculate enrichment, etc.: $d37/enrich.py -l ligand-file -d decoy-file

...and atom and receptor atom can be calculated as the solvent affinity of a ligand atom weighted by the volume of the solvent displaced from the receptor atom ...affinity of Si and a fragmental volume of fi. The solvent affinity of the ligand atom is calculated as:

-v, --verbose lots of debugging output receptor input pdb file, (default: rec.pdb)

Create rec.pdb and xtal-lig.mol2 for the receptor and the ligand, and type: You can sometimes start from as little as a [[PDB]] file using [[be_blasti]].

This format is used for general molecule input and output of DOCK. Although previous versions of DOCK supported an extended PDB forma ...the SOLVATION record, that has the atomic desolvation information for the ligand atoms. The parameter read_mol_solvation can be used to read in this record.

This page describes simple protocols for receptor/active site and ligand minimization using Plop.<br> ..._hydrogens_to_your_ligand_and_convert_to_mol2_format Add hydrogens to your ligand and convert to mol2 format]

...ioactive conformation to get a score for the crystallographic pose of your ligand. This is described here: http://wiki.uoft.bkslab.org/index.php/Scoreopt [[File:Nz14 xtal vs dock.png|thumb|right|alt=Prediction by DOCK depicted in yellow

$ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 $ python interfilter.py -protein rec.crg.pdb -ligand poses.mol2 -residue ASP115A

...ocking. Mabye you want to increase the number of conformations sampled per ligand, or the force field used.<br> ...opy a file called omega.parm into the directory where you want to generate ligand conformations using dbgen.csh. You should find a template in $DOCK_BASE/dat

=Ligand File Input= Before you can dock a ligand, you will need atom

* Full dependency resolution means you can change any input or parameter file and type 'make' to generate all files that depend on that change (i.e. tart # rec.pdb: Prepared receptor file

...>', which you can read into ViewDOCK in chimera as a DOCK 4, 5, or 6 style file. ...run <tt>$mud/topdock.py -e</tt>. If one wants to create an <tt>.eel1</tt> file for a different subset of the molecules, first create the list of molecule

=Preparing a ligand= *the file containing the [http://www.daylight.com/smiles/ SMILES] strings should cont