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  1. AU="Husseini, Fouad S"
  2. AU=Mihailescu Rita
  3. AU="Marrone, Anna-Claire"
  4. AU=Mills Caitlyn L.
  5. AU=Badawi Alaa
  6. AU="Genki Katata"
  7. AU="Kseniya Shuturminska"
  8. AU="Herzler, Matthias"
  9. AU=Godfrey W A
  10. AU="Jester, Rebecca"
  11. AU="Olivier Potvin"
  12. AU="Rombos, Antonis"
  13. AU="Kristiansson, Erik"
  14. AU="Tanous, Fadi"
  15. AU="Zeng, Fa-Min"
  16. AU="Kapusta, Andrzej"
  17. AU=Hebron Michaeline
  18. AU="Delfini, Ana Cláudia"
  19. AU="Barham, Lawrence"

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  1. Artikel: Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors.

    Wan, Shunzhou / Potterton, Andrew / Husseini, Fouad S / Wright, David W / Heifetz, Alexander / Malawski, Maciej / Townsend-Nicholson, Andrea / Coveney, Peter V

    Interface focus

    2020  Band 10, Heft 6, Seite(n) 20190128

    Abstract: We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ... ...

    Abstract We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A
    Sprache Englisch
    Erscheinungsdatum 2020-10-16
    Erscheinungsland England
    Dokumenttyp Journal Article
    ISSN 2042-8898
    ISSN 2042-8898
    DOI 10.1098/rsfs.2019.0128
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A

    Potterton, Andrew / Husseini, Fouad S / Southey, Michelle W Y / Bodkin, Mike J / Heifetz, Alexander / Coveney, Peter V / Townsend-Nicholson, Andrea

    Journal of chemical theory and computation

    2019  Band 15, Heft 5, Seite(n) 3316–3330

    Abstract: Drug-target residence time, the length of time for which a small molecule stays bound to its receptor target, has increasingly become a key property for optimization in drug discovery programs. However, its in silico prediction has proven difficult. Here ...

    Abstract Drug-target residence time, the length of time for which a small molecule stays bound to its receptor target, has increasingly become a key property for optimization in drug discovery programs. However, its in silico prediction has proven difficult. Here we describe a method, using atomistic ensemble-based steered molecular dynamics (SMD), to observe the dissociation of ligands from their target G protein-coupled receptor in a time scale suitable for drug discovery. These dissociation simulations accurately, precisely, and reproducibly identify ligand-residue interactions and quantify the change in ligand energy values for both protein and water. The method has been applied to 17 ligands of the A
    Mesh-Begriff(e) Humans ; Ligands ; Molecular Dynamics Simulation ; Receptor, Adenosine A2A/chemistry ; Time Factors
    Chemische Substanzen Ligands ; Receptor, Adenosine A2A
    Sprache Englisch
    Erscheinungsdatum 2019-04-26
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.8b01270
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Simulation of Two-Dimensional Infrared Spectroscopy of Peptides Using Localized Normal Modes.

    Hanson-Heine, Magnus W D / Husseini, Fouad S / Hirst, Jonathan D / Besley, Nicholas A

    Journal of chemical theory and computation

    2016  Band 12, Heft 4, Seite(n) 1905–1918

    Abstract: Nonlinear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and ... ...

    Abstract Nonlinear two-dimensional infrared spectroscopy (2DIR) is most commonly simulated within the framework of the exciton method. The key parameters for these calculations include the frequency of the oscillators within their molecular environments and coupling constants that describe the strength of coupling between the oscillators. It is shown that these quantities can be obtained directly from harmonic frequency calculations by exploiting a procedure that localizes the normal modes. This approach is demonstrated using the amide I modes of polypeptides. For linear and cyclic diamides and hexapeptide Z-Aib-L-Leu-(Aib)2-Gly-Aib-OtBu, the computed parameters are compared with those from existing schemes, and the resulting 2DIR spectra are consistent with experimental observations. The incorporation of conformational averaging of structures from molecular dynamics simulations is discussed, and a hybrid scheme wherein the Hamiltonian matrix from the quantum chemical local-mode approach is combined with fluctuations from empirical schemes is shown to be consistent with experiment. The work demonstrates that localized vibrational modes can provide a foundation for the calculation of 2DIR spectra that does not rely on extensive parametrization and can be applied to a wide range of systems. For systems that are too large for quantum chemical harmonic frequency calculations, the local-mode approach provides a convenient platform for the development of site frequency and coupling maps.
    Mesh-Begriff(e) Amides/chemistry ; Glycine/analogs & derivatives ; Glycine/chemistry ; Molecular Dynamics Simulation ; Peptides/chemistry ; Quantum Theory ; Spectrophotometry, Infrared/methods
    Chemische Substanzen Amides ; Peptides ; acetylglycyl-N-methylamide (7606-79-3) ; Glycine (TE7660XO1C)
    Sprache Englisch
    Erscheinungsdatum 2016-04-12
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1549-9626
    ISSN (online) 1549-9626
    DOI 10.1021/acs.jctc.5b01198
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Computing infrared spectra of proteins using the exciton model.

    Husseini, Fouad S / Robinson, David / Hunt, Neil T / Parker, Anthony W / Hirst, Jonathan D

    Journal of computational chemistry

    2016  Band 38, Heft 16, Seite(n) 1362–1375

    Abstract: The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a ... ...

    Abstract The ability to compute from first principles the infrared spectrum of a protein in solution phase representing a biological system would provide a useful connection to atomistic models of protein structure and dynamics. Indeed, such calculations are a vital complement to 2DIR experimental measurements, allowing the observed signals to be interpreted in terms of detailed structural and dynamical information. In this article, we have studied nine structurally and spectroscopically well-characterized proteins, representing a range of structural types. We have simulated the equilibrium conformational dynamics in an explicit point charge water model. Using the resulting trajectories based on MD simulations, we have computed the one and two dimensional infrared spectra in the Amide I region, using an exciton approach, in which a local mode basis of carbonyl stretches is considered. The role of solvent in shifting the Amide I band (by 30 to 50 cm
    Mesh-Begriff(e) Amides/chemistry ; Models, Theoretical ; Molecular Dynamics Simulation ; Protein Conformation ; Proteins/chemistry ; Solvents/chemistry ; Spectrophotometry, Infrared/methods ; Structure-Activity Relationship ; Water/chemistry
    Chemische Substanzen Amides ; Proteins ; Solvents ; Water (059QF0KO0R)
    Sprache Englisch
    Erscheinungsdatum 2016-11-21
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1479181-X
    ISSN 1096-987X ; 0192-8651
    ISSN (online) 1096-987X
    ISSN 0192-8651
    DOI 10.1002/jcc.24674
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel: Examining the role of protein structural dynamics in drug resistance in

    Shaw, Daniel J / Hill, Rachel E / Simpson, Niall / Husseini, Fouad S / Robb, Kirsty / Greetham, Gregory M / Towrie, Michael / Parker, Anthony W / Robinson, David / Hirst, Jonathan D / Hoskisson, Paul A / Hunt, Neil T

    Chemical science

    2017  Band 8, Heft 12, Seite(n) 8384–8399

    Abstract: Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new ... ...

    Abstract Antimicrobial resistance represents a growing global health problem. The emergence of novel resistance mechanisms necessitates the development of alternative approaches to investigate the molecular fundamentals of resistance, leading ultimately to new strategies for counteracting them. To gain deeper insight into antibiotic-target interactions, the binding of the frontline anti-tuberculosis drug isoniazid (INH) to a target enzyme, InhA, from
    Sprache Englisch
    Erscheinungsdatum 2017-10-16
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 2559110-1
    ISSN 2041-6539 ; 2041-6520
    ISSN (online) 2041-6539
    ISSN 2041-6520
    DOI 10.1039/c7sc03336b
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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