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  1. Article ; Online: PepTraq: a toolbox for in silico data mining and fast sequence filtering.

    Zanuttini, Bruno / Henry, Joël / Couronne, Christophe / Ouali, Abdelkader / Robert, Véronique / Zatylny-Gaudin, Céline

    Amino acids

    2023  Volume 55, Issue 5, Page(s) 709–712

    Abstract: The development of de novo sequencing tools has led to the massive production of genomes and transcriptomes from many unconventional animal models. To tackle this huge flow of data, PepTraq brings together many functionalities generally scattered in ... ...

    Abstract The development of de novo sequencing tools has led to the massive production of genomes and transcriptomes from many unconventional animal models. To tackle this huge flow of data, PepTraq brings together many functionalities generally scattered in multiple tools, so that sequences can be filtered on the basis of multiple criteria. It is particularly suitable for the identification of non-annotated transcripts, re-annotation, extraction of secretomes, neuropeptidomes, targeted search for peptides and proteins, preparing specific proteomics/peptidomics fasta files for mass spectrometry (MS) applications, MS data processing, etc. PepTraq is developed in Java, and is available as a desktop application that can be downloaded from https://peptraq.greyc.fr . It is also available as a web application at the same URL for processing small files (10-20 MB). The source code is open under a CeCILL-B licence.
    MeSH term(s) Animals ; Proteins/chemistry ; Software ; Peptides ; Mass Spectrometry/methods ; Data Mining
    Chemical Substances Proteins ; Peptides
    Language English
    Publishing date 2023-03-08
    Publishing country Austria
    Document type Journal Article
    ZDB-ID 1121341-3
    ISSN 1438-2199 ; 0939-4451
    ISSN (online) 1438-2199
    ISSN 0939-4451
    DOI 10.1007/s00726-023-03251-y
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Book ; Online: Exploiting complex pattern features for interactive pattern mining

    Hien, Arnold / Loudni, Samir / Aribi, Noureddine / Ouali, Abdelkader / Zimmermann, Albrecht

    2022  

    Abstract: Recent years have seen a shift from a pattern mining process that has users define constraints before-hand, and sift through the results afterwards, to an interactive one. This new framework depends on exploiting user feedback to learn a quality function ...

    Abstract Recent years have seen a shift from a pattern mining process that has users define constraints before-hand, and sift through the results afterwards, to an interactive one. This new framework depends on exploiting user feedback to learn a quality function for patterns. Existing approaches have a weakness in that they use static pre-defined low-level features, and attempt to learn independent weights representing their importance to the user. As an alternative, we propose to work with more complex features that are derived directly from the pattern ranking imposed by the user. Learned weights are then aggregated onto lower-level features and help to drive the quality function in the right direction. We explore the effect of different parameter choices experimentally and find that using higher-complexity features leads to the selection of patterns that are better aligned with a hidden quality function while not adding significantly to the run times of the method. Getting good user feedback requires to quickly present diverse patterns, something that we achieve but pushing an existing diversity constraint into the sampling component of the interactive mining system LetSip. Resulting patterns allow in most cases to converge to a good solution more quickly. Combining the two improvements, finally, leads to an algorithm showing clear advantages over the existing state-of-the-art.
    Keywords Computer Science - Artificial Intelligence
    Subject code 006
    Publishing date 2022-04-08
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: The main geothermal reservoirs in the south Algeria and their interest for local economic development

    Ait-Ouali Abdelkader / Ouali Salima / Hadjiat MM / Imessad Khaled

    E3S Web of Conferences, Vol 80, p

    2019  Volume 01006

    Abstract: The study area is one of the important geothermal provinces in south Algeria. It is characterized by a hot arid climate with intense dryness and very high evaporation rates. The Albian geothermal system is exploited by the wells mainly for domestic and ... ...

    Abstract The study area is one of the important geothermal provinces in south Algeria. It is characterized by a hot arid climate with intense dryness and very high evaporation rates. The Albian geothermal system is exploited by the wells mainly for domestic and agricultural purposes. The sandstone Continental Intercalary (CI) formation constitutes the reservoir for the Albian aquifer, covering an area of 600,000 km2. This reservoir is covered by calcareous formations which yield the chemical characteristics of highly mineralized Na-Cl type representing the deep thermal waters and Ca-SO4 type determined the presence of evaporate lithology . For a better understanding of geothermal reservoir characteristic, a multidisciplinary approach was adopted, including hydrogeochemistry and geothermometry. More than fifty samples collected from wells recently in 2017 with a temperature average between 38 and 60° C and conductivities range from 2010 to 3460 μS/cm. Geochemical analysis of those thermal waters exhibits a certain degree of salinity with sodium-chloride type waters domination. The maximal geothermal reservoir temperature estimated using geothermometry is about 120°C.
    Keywords Environmental sciences ; GE1-350
    Subject code 550
    Language English
    Publishing date 2019-01-01T00:00:00Z
    Publisher EDP Sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: New Pharmacophore Fingerprints and Weight-matrix Learning for Virtual Screening. Application to Bcr-Abl Data.

    Rehioui, Hajar / Cuissart, Bertrand / Ouali, Abdelkader / Lepailleur, Alban / Lamotte, Jean-Luc / Bureau, Ronan / Zimmermann, Albrecht

    Molecular informatics

    2022  Volume 42, Issue 1, Page(s) e2200210

    Abstract: In this work, we propose to analyze the potential of a new type of pharmacophoric descriptors coupled to a novel feature transformation technique, called Weight-Matrix Learning (WML, based on a feed-forward neural network). The application concerns ... ...

    Abstract In this work, we propose to analyze the potential of a new type of pharmacophoric descriptors coupled to a novel feature transformation technique, called Weight-Matrix Learning (WML, based on a feed-forward neural network). The application concerns virtual screening on a tyrosine kinase named BCR-ABL. First, the compounds were described using three different families of descriptors: our new pharmacophoric descriptors, and two circular fingerprints, ECFP4 and FCFP4. Afterwards, each of these original molecular representations were transformed using either an unsupervised WML method or a supervised one. Finally, using these transformed representations, K-Means clustering algorithm was applied to automatically partition the molecules. Combining our pharmacophoric descriptors with supervised Weight-Matrix Learning (SWML
    MeSH term(s) Pharmacophore ; Fusion Proteins, bcr-abl/metabolism
    Chemical Substances Fusion Proteins, bcr-abl (EC 2.7.10.2)
    Language English
    Publishing date 2022-11-04
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2537668-8
    ISSN 1868-1751 ; 1868-1743
    ISSN (online) 1868-1751
    ISSN 1868-1743
    DOI 10.1002/minf.202200210
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  5. Article: Towards a partial order graph for interactive pharmacophore exploration: extraction of pharmacophores activity delta.

    Lehembre, Etienne / Giovannini, Johanna / Geslin, Damien / Lepailleur, Alban / Lamotte, Jean-Luc / Auber, David / Ouali, Abdelkader / Cremilleux, Bruno / Zimmermann, Albrecht / Cuissart, Bertrand / Bureau, Ronan

    Journal of cheminformatics

    2023  Volume 15, Issue 1, Page(s) 116

    Abstract: This paper presents a novel approach called Pharmacophore Activity Delta for extracting outstanding pharmacophores from a chemogenomic dataset, with a specific focus on a kinase target known as BCR-ABL. The method involves constructing a Hasse diagram, ... ...

    Abstract This paper presents a novel approach called Pharmacophore Activity Delta for extracting outstanding pharmacophores from a chemogenomic dataset, with a specific focus on a kinase target known as BCR-ABL. The method involves constructing a Hasse diagram, referred to as the pharmacophore network, by utilizing the subgraph partial order as an initial step, leading to the identification of pharmacophores for further evaluation. A pharmacophore is classified as a 'Pharmacophore Activity Delta' if its capability to effectively discriminate between active vs inactive molecules significantly deviates (by at least δ standard deviations) from the mean capability of its related pharmacophores. Among the 1479 molecules associated to BCR-ABL binding data, 130 Pharmacophore Activity Delta were identified. The pharmacophore network reveals distinct regions associated with active and inactive molecules. The study includes a discussion on representative key areas linked to different pharmacophores, emphasizing structure-activity relationships.
    Language English
    Publishing date 2023-11-29
    Publishing country England
    Document type Journal Article
    ZDB-ID 2486539-4
    ISSN 1758-2946
    ISSN 1758-2946
    DOI 10.1186/s13321-023-00782-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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