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https://github.com/unixjunkie/consent

ligand-based virtual screening with consensus queries
https://github.com/unixjunkie/consent

chemical chemoinformatics consensus ecfp4 fingerprint lbvs ligand maccs molprint2d ocaml

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ligand-based virtual screening with consensus queries

Host: GitHub
URL: https://github.com/unixjunkie/consent
Owner: UnixJunkie
License: gpl-3.0
Created: 2017-02-06T14:47:31.000Z (almost 8 years ago)
Default Branch: master
Last Pushed: 2023-10-27T00:00:20.000Z (about 1 year ago)
Last Synced: 2023-10-27T03:03:56.616Z (about 1 year ago)
Topics: chemical, chemoinformatics, consensus, ecfp4, fingerprint, lbvs, ligand, maccs, molprint2d, ocaml
Language: OCaml
Homepage:
Size: 144 KB
Stars: 7
Watchers: 3
Forks: 4
Open Issues: 0
Metadata Files:
- Readme: README.md
- License: LICENSE

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README

        # Consent

Chemoinformatics software for Ligand-Based Virtual Screening (LBVS)

using consensus queries.

Cf. the INSTALL file for instructions on how to install consent.

# I) Command line help

    lbvs_consent -s {sing|oppo|opti|real|know}

                 -q queries.{sdf|mol2|csv|ecfp4}

                 -db candidates.{sdf|mol2|csv|ecfp4}

      -s  consensus policy {sing|oppo|opti|real|know} (mandatory)

      -q  queries file (known actives; mandatory)

      -db  database to rank order (mandatory)

      -o  where to write scores (can be combined with -top)

      -n  consensus size; #known actives used to create query (optional;

               default=all molecules in query file)

      -top  how many top scoring molecules to write out (optional;

           default=all; must be combined with -o)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1006728.svg)](https://doi.org/10.5281/zenodo.1006728)

# II) Usage recommendation

Please cite the corresponding paper (https://doi.org/10.1186/s13321-017-0248-5)

in case you use this software and publish about your results

(Consensus queries in ligand-based virtual screening experiments.

F. Berenger, O. Vu and J., Meiler. Journal of Cheminformatics, November 2017).

The opportunist consensus policy (-s oppo) is recommended.

It works well with any fingerprint and is usually the best performing

method.

However, if you really need to go faster, here are some recommendations:

- MACCS fingerprint (166 bits): use the realistic policy (-s real); it will

  average the MACCS fingerprints of your known actives.

- ECFP4 fingerprint (2048 bits; folded; uncounted):

  use the optimist policy (-s opti); it will

  do a logical union of the fingerprints of your known actives.

- UMOP2D (unfolded MOLPRINT2D; uncounted): same as for ECFP4, use -s opti.

# III) How to encode your molecules

First, we need some SDF and MOL2 files.

The obabel command is provided by the Open Babel package

(cf. http://openbabel.org).

    obabel data/ARm_actives.smi -O data/ARm_actives.sdf

    obabel data/ARm_inactives.smi -O data/ARm_inactives.sdf

    obabel data/ARm_actives.smi -O data/ARm_actives.mol2

    obabel data/ARm_inactives.smi -O data/ARm_inactives.mol2

    cat data/ARm_actives.mol2 data/ARm_inactives.mol2 > data/ARm_database.mol2

## With the MACCS fingerprint

    lbvs_consent_ob_maccs data/ARm_actives.sdf > data/ARm_actives.maccs

    lbvs_consent_ob_maccs data/ARm_inactives.sdf > data/ARm_inactives.maccs

    cat data/ARm_actives.maccs data/ARm_inactives.maccs > data/ARm_database.maccs

## With the ECFP4 fingerprint

    lbvs_consent_ecfp4.py data/ARm_actives.sdf > data/ARm_actives.ecfp4

    lbvs_consent_ecfp4.py data/ARm_inactives.sdf > data/ARm_inactives.ecfp4

    cat data/ARm_actives.ecfp4 data/ARm_inactives.ecfp4 > data/ARm_database.ecfp4

## With the UMOP2D fingerprint

    lbvs_consent_mop2di -i data/ARm_database.mol2 > data/ARm_database.idx

    lbvs_consent_mop2de -idx data/ARm_database.idx -i data/ARm_database.mol2 -o data/ARm_database.mop2d

# IV) How to query with a consensus query and a consensus policy

    # example with ECFP4 fingerprints and 20 actives

    head -20 data/ARm_actives.ecfp4 > data/ARm_query_20.ecfp4

    # recommended way; AUC ~= 0.60

    lbvs_consent -s oppo -q data/ARm_query_20.ecfp4 -db data/ARm_database.ecfp4 -o scores.txt

    # faster, but still with good performance in many cases; AUC ~= 0.61

    lbvs_consent -s opti -q data/ARm_query_20.ecfp4 -db data/ARm_database.ecfp4 -o scores.txt