DockRMSD

Abstract

Docked Root-mean-square deviation of atomic positions Paper

DockRMSD is capable of deterministically identifying the minimum symmetry-corrected RMSD and is able to do so without significant loss of computational efficiency compared to other methods. The open-source DockRMSD program can be conveniently integrated with various docking pipelines to assist with accurate atomic mapping and RMSD calculations, which can therefore help improve docking performance, especially for ligand molecules with complicated structural symmetry

Descriptions

=\sqrt{\frac{1}{n}\sum_{i=1}^n|vi-w_i|^2}=\sqrt{\frac{1}{n}\sum{i=1}^n((v{ix}-w{ix})^2+(v{iy}-w{iy})^2+(v{iz}-w{iz})^2})})

Paper extract

Computer-aided drug design, in particular protein–ligand docking, has brought about the discovery of many biologically active drugs [1, 2]. In many protein–ligand docking programs, a flexible small molecule structure is docked in a rigid protein receptor structure in order to find the optimal binding conformation and affinity of the small molecule within the protein binding pocket. Since the ability of these programs to accurately assess binding affinity is dependent on their ability to find the optimal conformation of the ligand in the protein binding pocket, docking programs are often benchmarked by their ability to reproduce the native binding pose of a ligand from a protein–ligand complex crystal structure. A common metric used to evaluate distance between the predicted pose and the native pose, given a superposition of their protein receptor structures, is the root mean square deviation (RMSD) between their respective atoms

DockRMSD PDF paper

Usage

Please use mamba for fast download and installation

conda install mamba -n base -c conda-forge

Local Install

*NIX systems only:
Linux and MacOS

Remove all previous pydockrmsd installation

If you have MacOS with apple silicon ‘M’ processor, please use manual installation.
Github Action cannot handle apple silicon yet

pip uninstall pydockrmsd

mamba env create --name pydockrmsd --file condaenv/requirement.yml
conda activate pydockrmsd
mamba env update --name pydockrmsd --file condaenv/ci-cd.yml --prune
./scripts/install.sh

Pypi install

Build Requirement

pip install -r requirements.txt

Direct Download

pip install pydockrmsd # pypi source

Example

• crystal_bench.py
  • rdkit, pandas, numpy, pyarrow required
• crystal_bench.ipynb
  DockRMSD Website python Wrapper: docking pose distance calculation

Python atom mapping and RMSD calculation of symmetric molecules through graph isomorphism. Journal of Cheminformatics, 11:40 (2019).

PyDockRMSD Written by Barre Kevin, DockRMSD Written by Eric Bell

Os supported

• Linux
• Mac OS
• Windows

Tools used

• cython
• pdoc3
• pandoc
• pandas
• pyarrow (file.parquet as file storage system)
• cibuildwheel (cross compilation)

Documentation

Simple Usage

from pydockrmsd.dockrmsd import PyDockRMSD
import pydockrmsd.hungarian as hungarian
dockrmsd = PyDockRMSD("./data/targets/1a8i/crystal.mol2",
                      "./data/targets/1a8i/vina1.mol2")
print(dockrmsd.rmsd)
print(dockrmsd.total_of_possible_mappings)
print(dockrmsd.optimal_mapping)
print(dockrmsd.error)
print(hungarian("./data/targets/1a8i/crystal.mol2",
                "./data/targets/1a8i/vina1.mol2"))

License

This project is open source licensed under the EUROPEAN UNION PUBLIC LICENCE v. 1.2 EUPL © the European Union 2007, 2016 License. Please see the LICENSE for more information.

Local documentation

pdoc3 pydockrmsd --http localhost:8080

Tag:

• v: Version
• d: Documentation
• b: Build
• p: Publish
• t: Test

Issues

Corresponding issues:

• neudinger/pyDockRMSD#3

CHANGELOG