General synopsis for running the utilities implemented in X-Score
FixPDB: preparing protein molecules in PDB format
FixMol2: preparing ligand molecules in Mol2 format
LogP: computing octanol-water partition coefficients
Started from version 1.2, a number of miscellaneous utilities have been implemented in X-Score. These utilities are designed to help the users in many ways.
The general synopsis for running a certain utility in X-Score is:
xscore -function input_file(s) output_file(s)
Here the "-function" flag tells the program what to do. Different functions may require different inputs and outputs, which will be explained below.
2. FixPDB: preparing protein molecules in PDB format
This function is designed to process a given PDB file and save it in the correct format for X-Score. It is HIGHLY recommended to use a PDB file that has been processed by this function as the RECEPTOR_PDB_FILE when running X-Score.
To run this function:
xscore -fixpdb the_input_PDB_file the_output_PDB_file
Basically, this function will do the following jobs. (1) Extract the information that is useful for X-Score computation from the given PDB file, including sequence and atom information, and sort them in the right format. (2) Identify common mistakes in atom naming and correct them according to standard PDB conventions. If the X-Score program cannot recognize certain atoms, such as a non-standard amino acid residue or a ligand molecule, they will be neglected and not written to the output PDB file. (3) Delete water molecules and inorganic ions that are far away from the protein molecule since they are irrelevant. (4) Keep only polar hydrogen atoms and neglecting non-polar hydrogen atoms. (5) Re-number all of the valid atoms, including ATOMs and HETATMs, continuously started from 1. The residue numbers are kept unchanged so that the users can still find a particular residue conveniently by its original assigned residue number. .
Note that the "FixPDB" function can only refine a PDB file. Before applying it, you are still supposed to do some basic editing work, such as deleting the ligand molecule(s) (if you are working on a complex structure) and add hydrogen atoms.
3. FixMol2: preparing ligand molecules in Mol2 format
This function is designed to process a given Mol2 file and save it in the correct format for X-Score. It is HIGHLY recommended to use a Mol2 file that has been processed by this function as the LIGAND_MOL2_FILE when running X-Score. This is especially important if X-Score is going to be applied to score a library of various molecules.
To run this function:
xscore -fixmol2 the_input_Mol2_file the_output_Mol2_file
Basically, this function will do the following jobs. (1) Extract the information that is useful for X-Score computation from the given Mol2 file, including atom and bond information. (2) Identify errors in atom typing and bond typing and correct them according to the standard Tripos conventions. Note that this function is able to identify and correct some common errors in atom typing and bond typing but certainly cannot handle all possible situations. We are still working on this function to make it more powerful. (3) If the X-Score program does not have proper parameters for certain atoms in the given molecule, such as Be, B, Si, and metal atoms, this molecule will be neglected and will not be written to the resulting Mol2 file.
4. LogP: computing octanol-water partition coefficients
Maybe you have already noticed that the XLOGP2 algorithm is fully implemented in X-Score, which computes logP values using an atom-additive algorithm plus some correction factors. You may compute the logP values of some given molecules simply by:
xscore -logp the_input_Mol2_file
The input Mol2 file may contain a single or multiple molecules. Results will be output on the screen. A log file named as "xlogp.log" will be created under your working directory, which tabulates the detailed information of each computed molecule (click here to view an example).
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