Automated generation of residue library entries for CYANA structure calculations in drug design
Abstract
Computational techniques have been important tools in pharmaceutical research and development, e.g. for the predictions of the interactions between drug candidates and target proteins. Among these techniques, the Combined assignment and dynamics algorithm for NMR applications (CYANA) software has been shown to be highly suited for protein structure determination. This manuscript explains a technique for automated generation of residue library entries for the software CYANA structure calculations in drug design. The entries of the PDB mmCIF chemical component dictionary are converted into the specific CYANA residue library format, which then can be used automatically in the structure determination of the CYANA software. One application of this project relies in pharmaceutical industry if Nuclear Magnetic Resonance (NMR) is used for experiments. This project will support new studies in the drug design by allowing the use of CYANA software automatically for any residue, which is present in PDB mmCIF chemical component dictionary. Further applications include the three dimensional structure calculation of any peptides and proteins whose residue entries are present inside the PDB Protein Data Bank.
User's Manual
This program is delivered using the tar file format (chemicalcomponent.tar) and gzip compressed (chemicalcomponent.tar.gz). After changing the current directory to the directory where the file chemicalcomponent.tar.gz is downloaded, the following command can be used to unpack the source code:
tar –xzf chemicalcomponent.tar.gz
This command creates the chemicalcomponent directory under the current directory. The source files of the program and its Makefile are under this chemicalcomponent directory. The current directory is changed to chemicalcomponent in the terminal by this command:
cd chemicalcomponent
After changing the directory into chemicalcomponent in the terminal, the following UNIX command should be run to compile the program:
make
This command creates the executable file of the program that is called chemicalcomponent. The program can be executed by using the following command:
./chemicalcomponent [options]
The options of the program are explained here:
| –f FILE | Read FILE as an input PDB file. Its default value is residue_entry. |
| -aa | The molecule is an amino acid. |
| -n | Add overlap atoms only to the N- terminus of the molecule. |
| -c | Add overlap atoms only to the C- terminus of the molecule. |
| -fba ATOMNAME | ATOMNAME is the first atom of the backbone. |
| -lba ATOMNAME | ATOMNAME is the last atom of the backbone. |
| -sc | Save all of the ring structures. |
| -nic | Use non-ideal Cartesian coordinates. |
| -info | Print the details of the running program to the screen. |
| -debug | Print all the steps and all the variable values to the screen. |
| -o FILE | Write the output, Cyana residue entry, to FILE. Its default value is INPUTFILE_cyana. |
| -np | Do not add any pseudo atoms to the structure |
| -help | Prints the program steps to the screen in runtime. |
The following command can be used to remove the files that are created by the make command:
make clean
