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      Physics-Inspired Structural Representations for Molecules and Materials

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          SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules

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            Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

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              CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

              The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems. (c) 2009 Wiley Periodicals, Inc.
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                Author and article information

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                Journal
                Chemical Reviews
                Chem. Rev.
                American Chemical Society (ACS)
                0009-2665
                1520-6890
                August 25 2021
                July 26 2021
                August 25 2021
                : 121
                : 16
                : 9759-9815
                Affiliations
                [1 ]Laboratory of Computational Science and Modeling, IMX, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
                [2 ]National Centre for Computational Design and Discovery of Novel Materials (MARVEL), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
                [3 ]Department of Physics and Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry CV4 7AL, United Kingdom
                [4 ]University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada
                [5 ]Engineering Laboratory, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
                Article
                10.1021/acs.chemrev.1c00021
                34310133
                0dff6577-a78c-499f-84b7-a069e38170a8
                © 2021

                https://creativecommons.org/licenses/by/4.0/

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