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Monomer structure fingerprints: an extension of the monomer composition version for peptide databases

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Abstract

Previously a fingerprint based on monomer composition (MCFP) of nonribosomal peptides (NRPs) has been introduced. MCFP is a novel method for obtaining a representative description of NRP structures from their monomer composition in a fingerprint form. An effective screening and prediction of biological activities has been obtained from Norine NRPs database. In this paper, we present an extension of the MCFP fingerprint. This extension is based on adding few columns into the fingerprint; representing monomer clusters, 2D structures, peptide categories, and peptide diversity. All these data have been extracted from the NRP structure. Experiments with Norine NRPs database showed that the extended MCFP, that can be called Monomer Structure FingerPrint (MSFP) produced high prediction accuracy (> 95%) together with a high recall rate (86%) obtained when MSFP was used for prediction and similarity searching. From this study it appeared that MSFP mainly built from monomer composition can substantially be improved by adding more columns representing useful information about monomer composition and 2D structure of NRPs.

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Funding

This work was supported by Lille University, CNRS and Programme national d’aide à l’Accueil en Urgence des Scientifiques en Exil (PAUSE).

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Authors and Affiliations

  1. Univ. Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, 59000, Lille, France

    Ammar Abdo & Maude Pupin

  2. Computer Science Department, Hodeidah University, Hodeidah, Yemen

    Ammar Abdo

  3. Computer Science Department, Aden Community College, Aden, Yemen

    Eissa Ghaleb

  4. Saad Al‐Abdullah Academy for Security Sciences, Al Kuwait, Kuwait

    Naser K. A. Alajmi

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  1. Ammar Abdo
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  2. Eissa Ghaleb
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  3. Naser K. A. Alajmi
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  4. Maude Pupin
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The research was conducted by mutual contributions of all authors. All authors read and approved the final manuscript.

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Correspondence to Ammar Abdo.

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Abdo, A., Ghaleb, E., Alajmi, N.K.A. et al. Monomer structure fingerprints: an extension of the monomer composition version for peptide databases. J Comput Aided Mol Des 34, 1147–1156 (2020). https://doi.org/10.1007/s10822-020-00336-8

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  • DOI: https://doi.org/10.1007/s10822-020-00336-8

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