As Described In The Accompanying Documentation

Db_COMBINE calculates the components of ligand-residue interaction energies as descriptors like COMBINE descriptors (Ortiz, et al., 1995). The interaction energies per residue are divided into van der Waals. Electrostatic contributions as described in Arakawa et al. . Subset Manager is the program for creating the subset of atoms. Changing the atatus of atoms by subset. The "machine.txt" file required by MOE/smp is generated from this selection. This imports an ASCII text file into a new MOE database, calculates the LogP for each record and then writes out another ASCII text file. This utility effectively removes those portions of a molecular surface pocket that obscure the view of the docked ligand. This file will have all of the data from the input database. Change the removeDuplicates option to 1 to enable this. Language. Press OK. So that the command above is executed instead of the default in the $mpu-rexec line. Make sure you can start MOE on all the machines by hand. // and that you have a user name and password to access data in it. // java -version at the command prompt of your computer. Find the largest binding pocket on a protein, without a GUI panel. Turn on the check boxes which you prefer. Click 'OK' or 'Apply'. If you clicked 'OK' button, the window would be closed. For example, if you have an HTS dataset and want to salvage false negatives. In that case, you can spot false negatives when they occur in the same clusters with multiple positives. This algorithm relies on distance geometry with subsequent forcefield refinement and backbone angle checks, stereochemistry checks, followed by knowledge potential scoring . You can then compute the aro_subst descriptor in MOE. After selecting 'Thickness' and 'Color', click 'Apply'. If 'Color' checkbox is turned off, the color of backbone is not changed. This rmsd and superposition tool takes into account molecular symmetry. This is the modified version of r-group clipping tool which clips off anything that is attached to the leaving group, along with the leaving group. It allows seamless navigation of designs. Access to quick tools. Moving your non-mouse hand off the keyboard. Onto a 3D mouse increases productivity. Runs SiteFinder and outputs the dummy atoms of the active sites into a pdb file. Computes the distance between centroids of sets of atoms. Note that an intermediate MOE database is NOT created in this code. All files in a given directory and its subdirectories are listed, with the full path prepended to each filename. In Windows NT/2K/XP, set it up as a service using the file $MOE/bin-i4w9/rexecd (rexecd -install).