Relevant bibliographies by topics / Semiempirical quantum-mechanical methods

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  2. Dissertations / Theses
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Academic literature on the topic 'Semiempirical quantum-mechanical methods'

Author: Grafiati
Published: 28 June 2021
Last updated: 17 February 2022

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Journal articles on the topic "Semiempirical quantum-mechanical methods"

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Diller, David J., Christine Humblet, Xiaohua Zhang, and Lance M. Westerhoff. "Computational alanine scanning with linear scaling semiempirical quantum mechanical methods." Proteins: Structure, Function, and Bioinformatics 78, no. 10 (May 13, 2010): 2329–37. http://dx.doi.org/10.1002/prot.22745.

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Řezáč, Jan, and Pavel Hobza. "Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods." Journal of Chemical Theory and Computation 8, no. 1 (December 22, 2011): 141–51. http://dx.doi.org/10.1021/ct200751e.

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Christensen, Anders S., Tomáš Kubař, Qiang Cui, and Marcus Elstner. "Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications." Chemical Reviews 116, no. 9 (April 13, 2016): 5301–37. http://dx.doi.org/10.1021/acs.chemrev.5b00584.

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Wollacott, Andrew M., and Kenneth M. Merz. "Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures." Journal of Chemical Theory and Computation 3, no. 4 (May 30, 2007): 1609–19. http://dx.doi.org/10.1021/ct600325q.

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Titmuss, Stephen J., Peter L. Cummins, Andrey A. Bliznyuk, Alistair P. Rendell, and Jill E. Gready. "Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions." Chemical Physics Letters 320, no. 1-2 (March 2000): 169–76. http://dx.doi.org/10.1016/s0009-2614(00)00215-3.

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Ibrahim, Mahmoud A. A. "Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study." Journal of Chemical Information and Modeling 51, no. 10 (September 26, 2011): 2549–59. http://dx.doi.org/10.1021/ci2002582.

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Kříž, Kristian, and Jan Řezáč. "Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design." Journal of Chemical Information and Modeling 60, no. 3 (February 15, 2020): 1453–60. http://dx.doi.org/10.1021/acs.jcim.9b01171.

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Yilmazer, Nusret Duygu, Pascal Heitel, Tobias Schwabe, and Martin Korth. "Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data." Journal of Theoretical and Computational Chemistry 14, no. 01 (February 2015): 1540001. http://dx.doi.org/10.1142/s0219633615400015.

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The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.
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Hostaš, Jiří, Jan Řezáč, and Pavel Hobza. "On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions." Chemical Physics Letters 568-569 (May 2013): 161–66. http://dx.doi.org/10.1016/j.cplett.2013.02.069.

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Titmuss, Stephen J., Peter L. Cummins, Alistair P. Rendell, Andrey A. Bliznyuk, and Jill E. Gready. "Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis." Journal of Computational Chemistry 23, no. 14 (September 4, 2002): 1314–22. http://dx.doi.org/10.1002/jcc.10122.

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Dissertations / Theses on the topic "Semiempirical quantum-mechanical methods"

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Williams, Duane E. "Parameterization of semiempirical quantum mechanical methods for the prediction of nuclear magnetic resonance chemical shifts in biologically relevant systems." [Gainesville, Fla.] : University of Florida, 2009. http://purl.fcla.edu/fcla/etd/UFE0024844.

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Kříž, Kristian. "Optimalizace semiempirických kvantově mechanických metod pro návrh léčiv in silico." Doctoral thesis, 2021. http://www.nusl.cz/ntk/nusl-445884.

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Optimization of Semiempirical Quantum Mechanical Methods for in Silico Drug Design Doctoral thesis Kristian Kříž The subject of this thesis is the optimization of semiempirical quantum mechanical methods (SQM) for their use in in silico drug design. The thesis covers two topics - COSMO2 solvation model optimization part and PLF547, PLA15 dataset development part. The first part is devoted to the optimization of COSMO solvation model by addition of a nonpolar term and reparametrization of the model for SQM methods PM6 and PM7. We have shown that the accuracy of the resulting "COSMO2" optimized model improved on all the tested datasets and we have compared it to other selected SQM solvation models. The method has also been tested on the protein ligand complexes as a part of a scoring function, where it provides better preditction of binding affinity of drug candidates for their target protein. The second part of the thesis describes the construction of datasets for noncovalent interactions aimed speicificly to represent an environment of an enyzme active site complexed with a ligand with reliable benchmark values of interaction energies in vacuum and solvent (water). The developed PLF547 and PLA15 datasets are suitable for testing and development of methods for the use in drug design. We have...
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Book chapters on the topic "Semiempirical quantum-mechanical methods"

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Kamp, Marc Willem. "Semiempirical Quantum Mechanical Methods." In Encyclopedia of Biophysics, 2309. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_274.

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Russo, N., and M. Toscano. "Some Applications of the Quantum-Mechanical Semiempirical Methods to the Gas-Phase Chemistry of Bio-Organic Ions." In Mass Spectrometry in the Biological Sciences: A Tutorial, 311–22. Dordrecht: Springer Netherlands, 1992. http://dx.doi.org/10.1007/978-94-011-2618-2_18.

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Journal articles
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