PLANTS-SPORES-pharmACOphore
- Indy Siva
Introduction
From: http://www.tcd.uni-konstanz.de/research/plants.php
In the drug development process, predicting the complex structure of a small ligand with a protein, the so-called protein-ligand-docking-problem, is extensively used in virtual screening of large databases and in lead optimization. Given a protein structure, a ligand structure and a scoring function, the goal is to find a low energy ligand conformation in the protein's binding site that corresponds to the global minimum of the scoring function. The docking algorithm PLANTS is based on a class of stochastic optimization algorithms called ant colony optimization (ACO). ACO is inspired by the behavior of real ants finding a shortest path between their nest and a food source. The ants use indirect communication in the form of pheromone trails which mark paths between the nest and a food source. In the case of protein-ligand docking, an artificial ant colony is employed to find a minimum energy conformation of the ligand in the binding site. These ants are used to mimic the behavior of real ants and mark low energy ligand conformations with pheromone trails. The artificial pheromone trail information is modified in subsequent iterations to generate low energy conformations with a higher probability.
Usage
module load plants/1.2 Command Usage: PLANTS --mode screen yourconfigfile
Plants 1.2 / SPORES (Structure PrOtonation and REcognition System) / pharmACOphore
Installation
mkidr -p /sw/plants/1.2/bin cp ../src/plants/PLANTS1.2_64bit . ln -s /sw/plants/1.2/bin/PLANTS1.2_64bit /sw/plants/1.2/bin/plants mkdir -p /sw/plants/1.2/doc cd /sw/plants/1.2/doc cp ../../1.2/src/plants/manual1.2.pdf . mkdir -p /sw/plants/spores/bin cp ../../1.2/src/plants/SPORES_64bit . ln -s /sw/plants/spores/bin/SPORES_64bit /sw/plants/spores/bin/spores mkdir -p /sw/plants/pharmacophore/bin cp ../../1.2/src/plants/pharmACOphore_64bit . chmod +x pharmACOphore_64bit
Sample PBS script
#!/bin/bash -l #PBS -m abe #PBS -V ### Mail to user #PBS -M YOUREMAIL@griffith.edu.au ### Job name #PBS -N PLANTS_test #PBS -l walltime=01:00:00 ### Number of nodes:Number of CPUs:Number of threads per node #PBS -l select=1:ncpus=1:mpiprocs=1 source $HOME/.bashrc module load plants/1.2 PLANTS --mode screen /export/home/s123456/yourconfigfile echo "Done with job"
Sample config file
# scoring function and search settings scoring_function chemplp search_speed speed1 # input protein_file /export/home/s123456/PLANTS_Dock/protein.mol2 ligand_file /export/home/s123456/PLANTS_Dock/180_0037.mol2 # output output_dir /export/home/s123456/PLANTS_Dock/180_0037 # write single mol2 files (e.g. for RMSD calculation) - Disabled for space issues. #write_multi_mol2 0 # binding site definition bindingsite_center 32.060 41.391 34.758 bindingsite_radius 12.000 # cluster algorithm cluster_structures 3 cluster_rmsd 2.0