This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project's goal is to make Chimera a good platform for preparing input for docking programs and for viewing/analyzing the output of such programs, most particularly UCSF DOCK but implemented in such a way as to not preclude use for other docking programs. Input preparation can include any or all of the following steps for a target receptor: - deleting bulk solvent - pruning alternate locations - changing selenomethinine to methionine - adding hydrogens - adding charges - compensating for missing areas of structure - writing Mol2-format input Output viewing and analysis includes the following abilities: - showing ligands in the context of the target receptor - sorting ligands based on score or subscore - filtering based on hydrogen bonds formed with the receptor - pruning the list of ligands and saving a pruned list Full information on the input-preparation tool (Dock Prep) can be found at: www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html Full information on the viewing/analysis tool (ViewDock) can be found at: www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/viewdoc
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