DOCKING SUPPORT IN CHIMERA

这个子项目是许多利用资源的研究子项目之一 由NIH/NCRR资助的中心拨款提供。子项目的主要支持 而子项目的主要调查员可能是由其他来源提供的， 包括其它NIH来源。 列出的子项目总成本可能 代表子项目使用的中心基础设施的估计数量， 而不是由NCRR赠款提供给子项目或子项目工作人员的直接资金。 这个项目的目标是使奇美拉一个很好的平台，为对接程序准备输入，并查看/分析这些程序的输出，特别是UCSF DOCK，但以这样一种方式实现，不排除用于其他对接程序。 输入准备可包括用于靶受体的以下步骤中的任一个或全部： - 删除散装溶剂 - 去离子 - 修剪备用位置 - 将金属原子用于X射线衍射的残留物改变为它们的"正常"对应物 - 加氢 - 添加费用 - 补偿结构缺失区域 - 写入Mol2格式输入 输出查看和分析包括以下功能： - 显示了靶受体背景下的配体 - 基于得分或子得分对配体进行排序 - 基于与受体形成的氢键的过滤 - 修剪配体列表并保存修剪后的列表 有关输入准备工具（Dock Prep）的完整信息，请访问：www.example.com 有关查看/分析工具（ViewDock）的完整信息，请访问：www.example.com

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: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockprep.html Full information on the viewing/analysis tool (ViewDock) can be found at: http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/viewdock/viewdock.html