Open AccessDissertation
Identifying prospective inhibitors against LdtMt5 from Mycobacterium tuberculosis as a potential drug target.
Victor Tinashe. Sabe
- 01 Jan 2018
5
TL;DR: This chapter discusses tuberculosis through the life cycle of Mycobacterium tuberculosis, followed by a discussion of quantum mechanics/molecular mechanics and its role in the tuberculosis burden.
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Abstract: ............................................................................................................................... ii DECLARATION: PLAGIARISM ......................................................................................... iv LIST OF PUBLICATIONS .................................................................................................... ix DEDICATION ........................................................................................................................ x ACKNOWLEDGEMENTS .................................................................................................... xi LIST OF ABBREVIATIONS ................................................................................................ xii LIST OF FIGURES .............................................................................................................. xv LIST OF TABLES ............................................................................................................... xvii Chapter 1 .................................................................................................................................. 18 Introduction .............................................................................................................................. 18 1.0 Background ......................................................................................................................... 18 1.1 Global Tuberculosis burden ................................................................................................ 18 1.1.1 Infection life cycle of Mycobacterium tuberculosis................................................................. 19 1.1.2 Mycobacteria cell wall ............................................................................................................. 20 1.1.2.1 The structural cell wall of Mycobacterium tuberculosis ....................................................... 20 1.1.2.2 Peptidoglycan layer of Mycobacterium tuberculosis ............................................................ 21 1.1.2.3 Transpeptidases and mycobacterial cell wall biosynthesis ................................................... 24 1.1.2.4 Inhibition of L,D Transpeptidase enzymes ........................................................................... 25 1.1.2.5 Computational studies on L,D Transpeptidase enzymes ...................................................... 25 1.2 Computational methods ...................................................................................................... 27 1.2.1 Virtual Screening ..................................................................................................................... 27 1.2.2 Molecular Dynamics (MD) Simulation ................................................................................... 29 1.2.3 Molecular Mechanics (MM) .................................................................................................... 30 1.2.4 Quantum Mechanics (QM) ...................................................................................................... 30 1.2.5 Hybrid quantum mechanics/molecular mechanics (QM/MM) ................................................ 31 1.2.5.1 ONIOM ................................................................................................................................. 32
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Citations
Guide To Protein Purification
Juliane Hahn
- 01 Jan 2016
TL;DR: This guide to protein purification is available in our digital library an online access to it is set as public so you can get it instantly.Thank you very much for downloading guide toprotein purification.
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TL;DR: This book covers the principle hydrodynamic and calorimetric techniques for studying protein-ligand interactions, which are fundamental for the protein to function properly.
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Computational Methods in Drug Discovery
TL;DR: Computer-aided drug discovery/design methods have played a major role in the development of therapeutically important small molecules for over three decades and theory behind the most important methods and recent successful applications are discussed.
ONIOM: A Multilayered Integrated MO + MM Method for Geometry Optimizations and Single Point Energy Predictions. A Test for Diels−Alder Reactions and Pt(P(t-Bu)3)2 + H2 Oxidative Addition
Mats Svensson,Stéphane Humbel,Robert D. J. Froese,Toshiaki Matsubara,and Stefan Sieber,Keiji Morokuma +5 more
TL;DR: In this article, a three-layered integrated molecular orbital and molecular mechanics (ONIOM) approach has been proposed and shown to be successful in reproducing benchmark calculations and experimental results.
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A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions
Lars Goerigk,Stefan Grimme +1 more
TL;DR: There is no statistical correlation between a functional's accuracy for atomization energies and the performance for chemically more relevant reaction energies, and it is shown that double-hybrids in general outperform those.
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Epik: a software program for pK a prediction and protonation state generation for drug-like molecules
John C. Shelley,Anuradha Cholleti,Leah L. Frye,Jeremy R. Greenwood,Mathew R. Timlin,Makoto Uchimaya +5 more
TL;DR: Extensions to the well-established Hammett and Taft approaches are used for pKa prediction, namely, mesomer standardization, charge cancellation, and charge spreading to make the predicted results reflect the nature of the molecule itself rather just for the particular Lewis structure used on input.
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Principles of docking: An overview of search algorithms and a guide to scoring functions
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