Comparison of similarity coefficients for chemical database retrieval

Mukhsin Syuib, Shereena M. Arif, Nurul Malim

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Citation (Scopus)

    Abstract

    Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.

    Original languageEnglish
    Title of host publicationProceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013
    PublisherInstitute of Electrical and Electronics Engineers Inc.
    Pages129-133
    Number of pages5
    ISBN (Print)9781479932511
    DOIs
    Publication statusPublished - 14 Nov 2014
    Event1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013 - Kota Kinabalu, Sabah
    Duration: 3 Dec 20135 Dec 2013

    Other

    Other1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013
    CityKota Kinabalu, Sabah
    Period3/12/135/12/13

    Fingerprint

    Similarity Coefficient
    Retrieval
    Fingerprint
    Molecules
    Screening
    Virtual Screening
    Drug Discovery
    Similarity Search
    Similarity Measure
    Computational Model
    Experiments
    Calculate
    Target
    Similarity
    Evaluation
    Coefficient
    Experiment
    Class

    Keywords

    • 2D fingerprints
    • Chemoinformatics
    • similarity measure
    • virtual screening

    ASJC Scopus subject areas

    • Computer Science(all)
    • Modelling and Simulation

    Cite this

    Syuib, M., Arif, S. M., & Malim, N. (2014). Comparison of similarity coefficients for chemical database retrieval. In Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013 (pp. 129-133). [6959906] Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/AIMS.2013.28

    Comparison of similarity coefficients for chemical database retrieval. / Syuib, Mukhsin; Arif, Shereena M.; Malim, Nurul.

    Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013. Institute of Electrical and Electronics Engineers Inc., 2014. p. 129-133 6959906.

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Syuib, M, Arif, SM & Malim, N 2014, Comparison of similarity coefficients for chemical database retrieval. in Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013., 6959906, Institute of Electrical and Electronics Engineers Inc., pp. 129-133, 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013, Kota Kinabalu, Sabah, 3/12/13. https://doi.org/10.1109/AIMS.2013.28
    Syuib M, Arif SM, Malim N. Comparison of similarity coefficients for chemical database retrieval. In Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013. Institute of Electrical and Electronics Engineers Inc. 2014. p. 129-133. 6959906 https://doi.org/10.1109/AIMS.2013.28
    Syuib, Mukhsin ; Arif, Shereena M. ; Malim, Nurul. / Comparison of similarity coefficients for chemical database retrieval. Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013. Institute of Electrical and Electronics Engineers Inc., 2014. pp. 129-133
    @inproceedings{fb25d6cd178e46a5a109434ace6b8ae3,
    title = "Comparison of similarity coefficients for chemical database retrieval",
    abstract = "Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.",
    keywords = "2D fingerprints, Chemoinformatics, similarity measure, virtual screening",
    author = "Mukhsin Syuib and Arif, {Shereena M.} and Nurul Malim",
    year = "2014",
    month = "11",
    day = "14",
    doi = "10.1109/AIMS.2013.28",
    language = "English",
    isbn = "9781479932511",
    pages = "129--133",
    booktitle = "Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013",
    publisher = "Institute of Electrical and Electronics Engineers Inc.",

    }

    TY - GEN

    T1 - Comparison of similarity coefficients for chemical database retrieval

    AU - Syuib, Mukhsin

    AU - Arif, Shereena M.

    AU - Malim, Nurul

    PY - 2014/11/14

    Y1 - 2014/11/14

    N2 - Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.

    AB - Similarity-based virtual screening is used in drug discovery by using computational model for rapid evaluation of large number of chemical molecules. Similarity searches use 2D or 3D fingerprints and similarity coefficient to calculate the structural resemblance between each molecule in a chemical database and a target structure. The objective of this work is to determine the best coefficient to be used in similarity searching to get the optimal results. This paper will describe the experiment to perform the molecular similarity searching using different similarity coefficients, which focus on 2D UNITY or ECFP4 fingerprint on 5 activity classes. We will also highlight the different similarity values and the optimal results of similarity measures. All this could depend on what type of fingerprint. As a conclusion, we found that every combination measure has its own advantage. But to look for the best possible results, the nature of molecular activity class could also play an important role.

    KW - 2D fingerprints

    KW - Chemoinformatics

    KW - similarity measure

    KW - virtual screening

    UR - http://www.scopus.com/inward/record.url?scp=84917694750&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=84917694750&partnerID=8YFLogxK

    U2 - 10.1109/AIMS.2013.28

    DO - 10.1109/AIMS.2013.28

    M3 - Conference contribution

    AN - SCOPUS:84917694750

    SN - 9781479932511

    SP - 129

    EP - 133

    BT - Proceedings - 1st International Conference on Artificial Intelligence, Modelling and Simulation, AIMS 2013

    PB - Institute of Electrical and Electronics Engineers Inc.

    ER -