Ultrafast shape and electrostatic ligand similarity search
LiraSearch is a tool / library for performing high-performance ligand similarity searches based on molecular shape and electrostatic potentials. It is designed for use in computational chemistry / drug discovery pipelines.
First of all, you can avoid installation completely by using the publicly available webserver at https://usegalaxy.eu/?tool_id=lirasearch. This also allows you access to the precomputed compound databases used for similarity search.
If you want to run via the command-line, the simplest way is to use the Docker container: docker pull sb17/lirasearch. This is used by the webserver above.
Or if you want to build the container yourself:
# Clone the repo
git clone https://github.com/gaintherapeutics/LiraSearch.git
cd LiraSearch/docker
docker build -t lirasearch:latest .After entering the container interactively with docker run -it sb17/lirasearch you can run the following commands:
python -m esp_dnn.predict -m ligand -i . -o . # predict ESP charges using the DNN method by Rathi et al., 2019, J. Med. Chem
esp-surface-generator ligand.pdb.pqr ligand.pdb.tmesh # calculate a tmesh file representing the ESP surface, code from the authors above
sh-coeff-calculator . # calculate spherical harmonics coefficientsYou can also run the LiraSearch code without using the container. First install Julia; you will also need to install the required dependencies with
julia -e 'using Pkg; Pkg.add.(["Glob", "Printf", "ArgParse", "TimerOutputs", "GeometryBasics", "ImplicitBVH", "Distributions"])'
For installation and running the ESP-DNN code, please see the repos of the original authors from Astex:
- https://github.com/AstexUK/ESP_DNN
- https://github.com/AstexUK/esp-surface-generator
- https://pubs.acs.org/doi/full/10.1021/acs.jmedchem.9b01129 (paper from J. Med. Chem.)
Starting from a directory containing tmesh files, run julia sh_coeffs.jl .. You can test in the example directory:
cd example
julia ../sh_coeffs.jl .
- Fork the repository
- Create a new branch (git checkout -b feature/foo)
- Write code
- Submit a pull request
Please raise issues on this GitHub repository.
This project is released under the MIT License.