PDB2ENTROPY and PDB2TRENT

Conformational and Translational-Rotational Entropy from Molecular Ensembles

Federico Fogolari, Ornela Maloku, Cedrix Jurgal Dongmo Foumthuim, Alessandra Corazza, Gennaro Esposito

    Research output: Contribution to journalArticle

    Abstract

    Entropy calculation is an important step in the postprocessing of molecular dynamics trajectories or predictive models. In recent years the nearest neighbor method has emerged as a powerful method to deal in a flexible way with the dimensionality of the problem. Here we provide two programs, PBD2ENTROPY and PDB2TRENT that compute the conformational and translational-rotational entropy, respectively, based on the nearest neighbor method. PDB2ENTROPY takes in input two files containing the following: (1) conformational ensembles of the same molecule(s) in PDB format and (2) definitions of torsion angles (a default file is provided where additional user definitions can be easily implemented). PDB2TRENT takes in a file containing samples of the complexed molecules, a string specifying atoms providing the reference framework to superimpose samples, and a string specifying atoms used to compute rotation and translation of one molecule with respect to the other. The C programs and sample demonstration data are available on the GitHub repository (URL: http://github.com/federico-fogolari/pdb2entropy and http://github.com/federico-fogolari/pdb2trent).

    Original languageEnglish (US)
    Pages (from-to)1319-1324
    Number of pages6
    JournalJournal of Chemical Information and Modeling
    Volume58
    Issue number7
    DOIs
    StatePublished - Jul 23 2018

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    Entropy
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    predictive model
    Torsional stress
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    ASJC Scopus subject areas

    • Chemistry(all)
    • Chemical Engineering(all)
    • Computer Science Applications
    • Library and Information Sciences

    Cite this

    PDB2ENTROPY and PDB2TRENT : Conformational and Translational-Rotational Entropy from Molecular Ensembles. / Fogolari, Federico; Maloku, Ornela; Dongmo Foumthuim, Cedrix Jurgal; Corazza, Alessandra; Esposito, Gennaro.

    In: Journal of Chemical Information and Modeling, Vol. 58, No. 7, 23.07.2018, p. 1319-1324.

    Research output: Contribution to journalArticle

    Fogolari, Federico ; Maloku, Ornela ; Dongmo Foumthuim, Cedrix Jurgal ; Corazza, Alessandra ; Esposito, Gennaro. / PDB2ENTROPY and PDB2TRENT : Conformational and Translational-Rotational Entropy from Molecular Ensembles. In: Journal of Chemical Information and Modeling. 2018 ; Vol. 58, No. 7. pp. 1319-1324.
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    abstract = "Entropy calculation is an important step in the postprocessing of molecular dynamics trajectories or predictive models. In recent years the nearest neighbor method has emerged as a powerful method to deal in a flexible way with the dimensionality of the problem. Here we provide two programs, PBD2ENTROPY and PDB2TRENT that compute the conformational and translational-rotational entropy, respectively, based on the nearest neighbor method. PDB2ENTROPY takes in input two files containing the following: (1) conformational ensembles of the same molecule(s) in PDB format and (2) definitions of torsion angles (a default file is provided where additional user definitions can be easily implemented). PDB2TRENT takes in a file containing samples of the complexed molecules, a string specifying atoms providing the reference framework to superimpose samples, and a string specifying atoms used to compute rotation and translation of one molecule with respect to the other. The C programs and sample demonstration data are available on the GitHub repository (URL: http://github.com/federico-fogolari/pdb2entropy and http://github.com/federico-fogolari/pdb2trent).",
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    AU - Dongmo Foumthuim, Cedrix Jurgal

    AU - Corazza, Alessandra

    AU - Esposito, Gennaro

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