Hotspots API

The Hotspots API is the Python package for the Fragment Hotspot Maps project, a knowledge-based method for determining small molecule binding "hotspots".

For more information on this method:

Radoux, C.J. et. al., Identifying the Interactions that Determine Fragment Binding at Protein Hotspots J. Med. Chem. 2016, 59 (9), 4314-4325 [dx.doi.org/10.1021/acs.jmedchem.5b01980]

Getting Started

Although the Hotspots API is publicly available, it is dependant on the CSD Python API - a commercial package.

If you are an academic user, it's likely your institution will have a license. If you are unsure if you have a license or would like to enquire about purchasing one, please contact [email protected].

Please note, this is an academic project and we would therefore welcome feedback, contributions and collaborations. If you have any queries regarding this package please contact us ([email protected])!

Installation

#1 Install CSDS 2019

Available from CCDC downloads page.

You will need a valid site number and confirmation code, this will have been emailed to you when you bought your CSDS 2019 license.

#2 Install GHECOM

Available from GHECOM download page.

The source code of the GHECOM is written in C, and developed and executed on the linux environment (actually on the Fedora Core). For the installation, you need the gcc compiler. If you do not want to use it, please change the "Makefile" in the "src" directory.

Download the file ghecom-src-[date].tar.gz file.

tar zxvf ghecom-src-[date].tar.gz
cd src
make
# The executable will be located at the parent directory ..

#3 Setup an Anaconda environment (recommended)

# create environment and install requirements
conda create -n hotspots python=2.7
conda install -n hotspots \
    numpy==1.15.4 matplotlib==2.2.3 scikit-image==0.14.2 \
    pandas==0.24.1 futures==3.2.0 cython==0.29.5 tqdm==4.31.1 \
    xmltodict==0.12.0 \
    scipy scikit-learn

# install the Python CSD API
conda install -n hotspots qt==5.9.7 rdkit==2018.09.1
conda install -n hotspots csd-python-api-2.x.x-linux-py2.7-conda.tar.bz2

# install Hotspots v1.0.0
conda run -n hotspots pip install https://github.com/prcurran/hotspots/archive/v1.0.0.zip

Hotspots API Usage

Start activating your Anaconda environment and setting some variables.

conda activate hotspots
export GHECOM_EXE=<path_to_GHECOM_executable>
export CSDHOME=<path_to_CSDS_installation>/CSD_2019

Running a Calculation

Protein Preparation

The first step is to make sure your protein is correctly prepared for the calculation. The structures should be protonated with small molecules and waters removed. Any waters or small molecules left in the structure will be included in the calculation.

One way to do this is to use the CSD Python API:

from ccdc.protein import Protein

prot = Protein.from_file('protein.pdb')
prot.remove_all_waters()
prot.add_hydrogens()
for l in prot.ligands:
    prot.remove_ligand(l.identifier)

For best results, manually check proteins before submitting them for calculation.

Calculating Fragment Hotspot Maps

Once the protein is prepared, the hotspots.calculation.Runner object can be used to perform the calculation:

from hotspots.calculation import Runner

runner = Runner()
results = runner.from_pdb(prot, nprocesses=11)

Alternatively, for a quick calculation, you can supply a PDB code and we will prepare the protein as described above:

runner = Runner()
results = runner.from_pdb("1hcl", nprocesses=11)

Reading and Writing Hotspots

Writing

The hotspots.hs_io module handles the reading and writing of both hotspots.calculation.results and `hotspots.best_volume.Extractor objects. The output .grd files can become quite large, but are highly compressible, therefore the results are written to a .zip archive by default, along with a PyMOL run script to visualise the output.

from hotspots.hs_io import HotspotWriter

out_dir = "results/pdb1"

# Creates "results/pdb1/out.zip"
with HotspotWriter(out_dir) as writer:
    writer.write(results)

Reading

If you want to revisit the results of a previous calculation, you can load the out.zip archive directly into a hotspots.calculation.results instance:

from hotspots.hs_io import HotspotReader

results = HotspotReader('results/pdb1/out.zip').read()

Using the Output

While Fragment Hotspot Maps provide a useful visual guide, the grid-based data can be used in other SBDD analysis.

Scoring

One example is scoring atoms of either proteins or small molecules.

This can be done as follows:

from ccdc.protein import Protein
from ccdc.io import MoleculeReader, MoleculeWriter
from hotspots.calculation import Runner

    r = Runner()
    prot = Protein.from_file("1hcl.pdb")    # prepared protein
    hs = r.from_protein(prot)

    # score molecule
    mol = MoleculeReader("mol.mol2")
    scored_mol = hs.score(mol)
    with MoleculeWriter("score_mol.mol2") as w:
        w.write(scored_mol)

    # score protein
    scored_prot = hs.score(hs.prot)
    with MoleculeWriter("scored_prot.mol2") as w:
        w.write(scored_prot)

To learn about other ways you can use the Hotspots API please see the examples directory and read our API documentation.