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      An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

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          Abstract

          Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.

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          Comparison of simple potential functions for simulating liquid water

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            CHARMM-GUI: a web-based graphical user interface for CHARMM.

            CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. 2008 Wiley Periodicals, Inc.
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              Protein folding and misfolding.

              The manner in which a newly synthesized chain of amino acids transforms itself into a perfectly folded protein depends both on the intrinsic properties of the amino-acid sequence and on multiple contributing influences from the crowded cellular milieu. Folding and unfolding are crucial ways of regulating biological activity and targeting proteins to different cellular locations. Aggregation of misfolded proteins that escape the cellular quality-control mechanisms is a common feature of a wide range of highly debilitating and increasingly prevalent diseases.
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                Author and article information

                Journal
                Chem Rev
                Chem. Rev
                cr
                chreay
                Chemical Reviews
                American Chemical Society
                0009-2665
                1520-6890
                27 January 2016
                11 May 2016
                : 116
                : 9 , Noncovalent Interactions
                : 4983-5013
                Affiliations
                []Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore , Baltimore, Maryland 21201, United States
                []Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States
                Author notes
                [* ]Mailing address: 20 Penn St., Room 633, Baltimore, MD 21201. E-mail: alex@ 123456outerbanks.umaryland.edu . Phone: (410) 706-7442. Fax: (410) 706-5017.
                Article
                10.1021/acs.chemrev.5b00505
                4865892
                26815602
                b9de93de-89e2-453a-8cca-5db652f45011
                Copyright © 2016 American Chemical Society

                This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.

                History
                : 31 August 2015
                Categories
                Review
                Custom metadata
                cr5b00505
                cr-2015-005053

                Chemistry
                Chemistry

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