RINRUS

Residue Interaction Network-based ResidUe Selector (RINRUS) is a QM-cluster model building tool for biomolecular systems. Starting from a raw PDB file, after running a series of preparation tasks, the tool will

select important residues for chemical reactions, and
generate trimmed PDB files with the corresponding quantum chemical inputs.

RINRUS is the first tool available that performs automated and algorithmic trimming and capping of enzyme models. Reproducibility is embedded into the model construction workflow, setting new community standards.

A software review paper is in preparation. For now, the best way to acknowledge RINRUS is to cite: DOI: 10.1016/j.bpj.2021.07.029 and DOI: 10.1039/D3CP06100K

The development of RINRUS has been supported by the National Science Foundation Division of Biological Infrastructure (CAREER BIO-1846408) and the Department of Energy Basic Energy Sciences (SBIR DE-SC0021568). If you have questions or would like to contribute to the development of RINRUS, please email Prof. Nathan DeYonker, Department of Chemistry, University of Memphis at ndyonker@memphis.edu

Installation

Clone this repository, then add the library code under lib3 to your PYTHONPATH. For example, in ~/git:

cd ~/git
git clone git@github.com:natedey/RINRUS.git
export PYTHONPATH="~/git/RINRUS/lib3:$PYTHONPATH"

Python dependencies

Python >= 3.x
NumPy
pymol
- If installing via conda, it's under -c conda-forge pymol-open-source.
openbabel (required for Arpeggio)
pandas

For certain scripts (optional),

matplotlib
BioPython

External dependencies

probe - version 2.16.130520 is packaged with RINRUS
reduce - version 3.23 is packaged with RINRUS
arpeggio
obabel version = openbabel/2.4.1

Currently, precompiled binaries of probe, reduce, and arpeggio are present in bin/.

which require

CMake >= 3.10
Any C/C++ compiler suite with C++11 support

PDB HET groups (some ligands and noncanonical amino acids) can be protonated by reduce. The connectivity table file is included with RINRIS: bin/reduce_wwPDB_het_dict.txt You must set a shell environment variable to allow reduce to use the reduce_wwPDB_het_dict file, as the default location is /local:

setenv REDUCE_HET_DICT /home/$USER/git/RINRUS/bin/reduce_wwPDB_het_dict.txt

export REDUCE_HET_DICT=/home/$USER/git/RINRUS/bin/reduce_wwPDB_het_dict.txt

Further preproccesing of ligands likely required!

How to use

To run the full workflow from initial protein PDB structure to QM software input file use the driver as described in driver/.

More detailed documentation/instructions for each step of the process is given in bin/.

Contributors

This code was conceptualized in the DeYonker group at the University of Memphis Department of Chemistry. Prof. Qianyi Cheng was the primary contributor to early versions of RINRUS, who now runs her independent research group at University of Memphis. Additional code, conceptualization, and documentation have been provided by Prof. Nathan DeYonker, Dr. Dominique Wappett, Dr. Thomas Summers, Dr. Donatus Agbaglo, Tejas Suhagia, Dr. Taylor Santaloci, Prof. Jose Fernando Ruggiero Bachega, (Universidade Federal de Ciências da Saúde de Porto Alegre), and Dr. Eric Berquist (Q-Chem, Inc.)

natedey / RINRUS

readme