jsdir / shchem

shchem

Live at https://shchem.herokuapp.com

Setup

Seeding the database

Setup Postgres

• If you want to run postgres locally: https://www.digitalocean.com/community/tutorials/how-to-install-and-use-postgresql-on-ubuntu-16-04

• Change the DATABASE_URL in .env to match the credentials of the running instance

  DATABASE_URL='postgres://gtiwrmbyatjafb:[e-mail]:5432/d3gsce3nipr26i'
  

Migrate

./node_modules/.bin/sequelize db:migrate

Begin uploading the compound data

For partially seeding the data locally, you can run:

npm run seed-compounds

In production, you'll want to use the job queue to seed the entire database. Change .env to the production settings, then run:

npm run seed-compounds-job

Open localhost:3000/job-queue to view the progress.

To run a partial seed, add a limit argument to process a fixed number of files. This is helpful for testing:

npm run seed-compounds-job 10

Updating the list of compound files

To update the list of component files, run:

cd seed
./generate_compound_files.sh

This pulls a list of files from ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/CURRENT-Full/ASN/

Running the app

You need the following environment variables:

• DATABASE_URL: path to your postgres database
• BABEL_PATH: path to the babel binary of Open Babel
• IDOCK_PATH: path to the idock binary of idock

Parser Information

• Pubchem schema: ftp://ftp.ncbi.nih.gov/pubchem/specifications/pubchem.xsd
• Example JSON record: https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/1650002/record/JSON/

Testing

To test everything:

npm test

To only test the client:

npm run test-client

To only test the server:

npm run test-server

Run server tests on file change:

npm run test-server -- -w

Docking

To run the worker:

• Setup a redis instance, then:

npm run worker

Other Resources

• Molecular Docking
  • Search/scoring algorithms
    • https://www.researchgate.net/profile/Raquel_Dias2/publication/23763093_Molecular_Docking_Algorithms/links/02e7e524de3bfd2b11000000.pdf (Table 1. Docking Algorithms)
    • bsp-slim
      • site: http://zhanglab.ccmb.med.umich.edu/BSP-SLIM
      • paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3240723
    • autodock vina
      • site: http://vina.scripps.edu
      • paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041641
      • source: https://github.com/jandom/autodock-vina
    • mcdock
      • paper: https://www.ncbi.nlm.nih.gov/pubmed/10483527
      • source: https://github.com/andersx/mcdock
  • Online Services
    • istar
      • paper: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0085678
      • engine: https://github.com/HongjianLi/idock
      • service: http://istar.cse.cuhk.edu.hk/idock
    • swissdock
      • paper: https://academic.oup.com/nar/article-pdf/39/suppl_2/W270/7628003/gkr366.pdf
      • service: http://www.swissdock.ch/docking
    • blaster
      • paper: http://pubs.acs.org/doi/pdf/10.1021/jm9006966
    • patchdock
      • paper: http://bioinfo3d.cs.tau.ac.il/PatchDock/wabi02.pdf
      • service: http://bioinfo3d.cs.tau.ac.il/PatchDock/index.html
  • Distributed docking simulations
    • Docking@Home
      • site: http://docking.cis.udel.edu
      • papers
        • https://gcl.cis.udel.edu/publications/conferences/13_CSE_zhang.pdf
        • http://dl.acm.org/citation.cfm?id=2305618
        • https://gcl.cis.udel.edu/publications/conferences/12_HPCC_paper.pdf
      • source
        • https://github.com/TauferLab
        • https://github.com/TauferLab/Data-Reduction-and-Octree-based-Clustering-of-Ligand-Conformations-in-MRMPI
    • AutoDockCloud
      • paper: http://dl.acm.org/citation.cfm?id=2768050
    • wfredow
      • paper: https://www.hindawi.com/journals/bmri/2013/469363