X-ToolBox是由中国科学院上海有机化学研究所王任小研究员课题组发展的一套程序软件，用于处理蛋白分子以及有机小分子的结构文件，配合应用其他计算蛋白-配体相互作用的计算化学软件（例如本课题组开发的X-Score等软件）。X-ToolBox可以处理存储蛋白分子结构的PDB格式文件以及存储有机小分子结构的MOL2格式和SDF格式文件，去除其中不必要的内容，并能自动鉴别和修正一些原子类型以及化学键类型中的错误，最终输出格式规范的PDB、MOL2或SDF格式文件。另外，X-ToolBox软件依据“氢键作用最大化”算法，可以预测蛋白-配体复合物中特定基团的质子化状态。与现有类似商业软件或学术软件相比，X-ToolBox实现了较高的预测精度。         
[user manual]
Upload Structure Files
Protein:   (PDB format)
Small Molecule:   (mol2/sdf format)
Select Functions
Use Module:
  
Notes:
  1. When predicting protonation status, you can provide a protein (PDB file format) or with a ligand (mol2 file format).
  2. When fixing protein PDB file, you can only provide a protein (PDB file format), other parameters will be ignored.
  3. When fixing ligand Mol2 file, you can only provide a ligand (mol2 file format), other parameters will be ignored.
  4. When fixing ligand SDF file, you can only provide a ligand (SDF file format), other parameters will be ignored.
Reference:
  1. Li Y.; Han L.; Liu Z.H.; Wang R.X.*, "Comparative Assessment of Scoring Functions on an Updated Benchmark: II. Evaluation Methods and General Results", J. Chem. Inf. Model., 2014, 54 (6), pp. 1717-1736.
  2. Li Y.; Liu Z.H.; Li J.; Han L.; Liu J.; Zhao Z.X.; Wang R.X.*, "Comparative Assessment of Scoring Functions on an Updated Benchmark: I. Compilation of the Test Set", J. Chem. Inf. Model., 2014, 54 (6), pp. 1700-1716.
  3. Zhang, X.; Li, X.; Wang, R. X.*, "Interpretation of the Binding Affinities of PTP1B Inhibitors with the MM-GB/SA method and the X-Score Scoring Function", J. Chem. Inf. Model., 2009, Vol. 49, pp 1033-1048. (cover story)