User contributions for Frodo
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13 February 2014
- 21:4021:40, 13 February 2014 diff hist +1,567 N Running DOCK 3.7 Created page with "Setting up an alias for the dock37tools directory in $DOCK_BASE/src/dock37tools/ is highly recommended, though you don't need it if you don't want it. Assume you have it set a..." current
- 21:3921:39, 13 February 2014 diff hist +4 DOCK 3.7 No edit summary
- 21:3821:38, 13 February 2014 diff hist +555 N ZINC Subset DB2 file locations Created page with "On the UCSF cluster: /raida/db/rgc/frags-now-marvin Fragments available now /raida/db/rgc/frags-all-marvin All fragments available now or on-demand quickly /raida/db/rgc/lead..."
- 21:3721:37, 13 February 2014 diff hist +3,536 N Flexible Docking Created page with """"Flexible Docking""" For citations and example use, please see Citations for DOCK3.7, Fischer, Coleman et al. Input for flexible docking requires a single PDB file with al..." current
- 21:3521:35, 13 February 2014 diff hist +672 N Adding Static Waters to the Protein Structure Created page with "If you have ordered waters in your structure, DOCK3.7 can use them, but you have to add hydrogens 'manually' using some visualization program and your intuition. Once this is ..."
- 21:3421:34, 13 February 2014 diff hist +1,669 N Protein Target Preparation Created page with "Protein Target Preparation be-blasti is still the preferred method of downloading PDB files and splitting them into rec.pdb and xtal-lig.pdb files. Run it with be_blasti.csh ..."
- 21:3121:31, 13 February 2014 diff hist +181 N Mol2db2 Created page with "mol2db2 is a program that takes multi-conformation mol2 files and compiles them into the db2 format for docking. {{Template:CC-BY-SA-30}} {{Template:Coleman}} [[Category:DOCK..."
- 21:3021:30, 13 February 2014 diff hist +2 DOCK 3.7 No edit summary
- 21:3021:30, 13 February 2014 diff hist +35 DOCK 3.7 No edit summary
- 21:2921:29, 13 February 2014 diff hist 0 Ligand preparation No edit summary
- 21:2821:28, 13 February 2014 diff hist +1,096 N Ligand preparation Created page with "Ligand preparation has been modified to use mol2db2 instead of mol2db for database generation. Many other features have also been integrated. To build a set of ligands from SM..."
- 21:2721:27, 13 February 2014 diff hist +6,248 N Mol2db2 format Created page with "<pre> Mol2db2 Format 2 File Format T type information (implicitly assumed) M molecule (4 lines req'd, after that they are optional, 24 lines max) A atoms B bond X xyz R rigid..."
- 21:2321:23, 13 February 2014 diff hist +4 DOCK 3.7 No edit summary
- 21:2221:22, 13 February 2014 diff hist +47 Analyzing DOCK 3.7 Results No edit summary current
- 21:2121:21, 13 February 2014 diff hist +4,710 N INDOCK 3.7 Created page with "<pre> DOCK 3.7 parameter ##################################################### # NOTE: split_database_index is reserved to specify a list of files ligand_atom_file ..."
- 21:1921:19, 13 February 2014 diff hist −2 DOCK 3.7 No edit summary
- 21:1821:18, 13 February 2014 diff hist +1 DOCK 3.7 No edit summary
- 21:1821:18, 13 February 2014 diff hist −25 DOCK 3.7 No edit summary
- 21:1721:17, 13 February 2014 diff hist +306 DOCK 3.7 No edit summary
- 21:1721:17, 13 February 2014 diff hist +175 N Template:Coleman Created page with "This page is adapted from "DOCK3.7 Documentation" by Ryan G. Coleman. Based on a work at [https://sites.google.com/site/dock37wiki/ https://sites.google.com/site/dock37wiki/]."