This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. 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 - deleting ions - pruning alternate locations - change residues where metal atoms were used for X-ray diffraction to their """"""""normal"""""""" counterparts - 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/viewdock.html
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