Dihedral Rotation Of Proteins (DROP)
Copyright 2023- Brian Andrews.
The repository contains a work-in-progress molecular mechanics command line tool which can manipulate protein structures by rotating dihedral angles and perform various analyses on the manipulated structures. It contains tools which are useful for preparing protein structures for visualizations in presentations, lectures, or papers and preparing protein structures for simulation. This tool will be used to investigate accessible regions of the high-dimensional conformation space of proteins based on atomic overlaps and generating mean fields from which dynamics simulations may be performed. The scope of this project will continue to expand over time with additional modules for analyzing and manipulating molecular structures. This is not a pdb (or any structure file) preprocessing tool. It requires a sanitized pdb file and currently requires CONECT records for covalent bonds for many functionalities. I personally use GROMACS (gitlab) to produce ordered pdb files and CONECT records. See scripts/generate-conect/ for more details. CONECT records are required for any calculation which requires knowledge of how many covalent bonds are between atoms in a chain.
After cloning the directory or downloading and unzipping a release, you can compile DROP with make in the parent directory.
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See commands:
./drop --help -
See command options:
./drop [command] --help
After compilation, you can export the path to the DROP executable to use the tool without the ./.
To measure the dihedral angles of a given structure, use measureDihedrals. To manipulate protein structures, you can use setDihedral or setDihedralList. The former allows for the modification of one dihedral angle and the latter allows the user to provide a list of dihedral angles in a file to change in the structure. First example for setDihedral:
./drop setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d phi -a -60 -o output.pdb
which changes the dihedral angle phi of residue 2 to -60 degrees. You can visualize output.pdb with your favorite visualization tool like VMD or PyMol. setDihedralList has examples in examples/setDihedralList/README.md, but here's an example command:
./drop setDihedralList -i examples/setDihedralList/Polyarginine/poly-R-beta.pdb -d examples/setDihedralList/Polyarginine/beta-to-helix.txt -o poly-R-helix.pdb
If trying to reproduce results from a specific paper below, you may find past versions, scripts, and raw data in the Releases tab.
- B. Andrews. Amino Acid Residue-Specific Ramachandran Distributions Derived from a Simple Mean Field Potential. Physical Chemistry Au. 2024. 10.1021/acsphyschemau.4c00064.
If you use this work for research or presentations, please consider citing this repository with the version indicated.
@software{Andrews_DROP_2024,
author = {Andrews, Brian},
title = {{Dihedral Rotation of Proteins (DROP)}},
url = {https://github.com/andrewsb8/DROP/tree/main},
year = {2024}
}
The indent package is used to format this code with the following command:
indent -kr -ts4 [input file]