/exprorer

EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation

Primary LanguageC++GNU General Public License v3.0GPL-3.0

EXPRORER

EXPRORER (EXtended PRObes set construction by REpresentative Retrieval) is a systematic procedure to construct a set of cosolvent for drug discovery [Yanagisawa].

This repository contains two parts of it:

  • cosolv_generator: Generation of cosolvent structures
    • Two sub-parts: compounds decomposition & substructure filtering
  • cmd_calculation: Calculation scripts for Cosolvent MDs
  • scp_solver: Construction of cosolvent sets
    • A minimum set cover problem solver based on [Beasley1990]

Overall requirements

Versions are an examples of an author's environment.

  • C++ (cosolv_generator, scp_solver)
    • Boost 1.69.0
    • Open Babel 2.4.1
      • Do not use the latest version, 3.0.0 or newer since we found the code did not work with it.
  • Python 3 (cosolv_generator)
    • RDKit 2020.03.1
    • OpenBabel 2.4.1 (Please DO NOT use 3.x.x)

As for cmd_calculation, requirements are shown in cmd_calculation/README.md.

Environment construction

This section shows an example of an author (Keisuke Yanagisawa) without administrator privileges (i.e. supercomputing system), and we do not guarantee the procedure works well or not in your computational environment.

C++

boost 1.69.0

cd /PATH/TO/TMPDIR
wget https://dl.bintray.com/boostorg/release/1.69.0/source/boost_1_69_0.tar.gz
tar -zxvf boost_1_69_0.tar.gz
cd boost_1_69_0
./bootstrap.sh
./b2 install --prefix=PATH/TO/BOOST/1_69_0 --without-python

echo "export BOOST_INSTALL_PATH=/PATH/TO/BOOST/1_69_0" >> ~/.bashrc
source ~/.bashrc
echo "export LD_LIBRARY_PATH=$BOOST_INSTALL_PATH/lib:$LD_LIBRARY_PATH" >> ~/.bashrc
source ~/.bashrc

Open Babel 2.4.1

cd /PATH/TO/TMPDIR
wget https://sourceforge.net/projects/openbabel/files/openbabel/2.4.1/openbabel-2.4.1.tar.gz/download -O openbabel-2.4.1.tar.gz
tar -zxvf openbabel-2.4.1.tar.gz
cd openbabel-2.4.1
mkdir -p build
cd build
cmake -DCMAKE_INSTALL_PREFIX=/PATH/TO/openbabel/2_4_1 .. 
make -j
make test
make install

echo "export OBABEL_INSTALL_PATH=/PATH/TO/openbabel/2_4_1" >> ~/.bashrc
source ~/.bashrc
echo "export LD_LIBRARY_PATH=$OBABEL_INSTALL_PATH/lib:$LD_LIBRARY_PATH" >> ~/.bashrc
source ~/.bashrc

Python 3

This example uses Anaconda (It is possible to use pip instead of it).

cd /PATH/TO/TMPDIR
wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
bash ./Anaconda3-2020.02-Linux-x86_64.sh
source ~/.bashrc

conda install rdkit=2020.03.1

Reference

[Beasley1990] Beasley JE. "A Lagrangian Heuristic for Set-Covering Problems", Nav Res Logist 37: 151-164, 1990.

[Yanagisawa2021] Yanagisawa K, Moriwaki Y, Terada T, Shimizu K, "EXPRORER: Rational Cosolvent Set Construction Method for Cosolvent Molecular Dynamics Using Large-Scale Computation", J Chem Inf Model 61: 2744-2753, 2021.