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      Thionation toward High-Contrast ACQ-DIE Probes by Reprogramming the Aqueous Segregation Behavior: Enlightenment from a Sulfur-Substituted G-Quadruplex Ligand

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          VMD: Visual molecular dynamics

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            AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.

            AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 development. Further speed-up is achieved from parallelism, by using multithreading on multicore machines. AutoDock Vina automatically calculates the grid maps and clusters the results in a way transparent to the user. Copyright 2009 Wiley Periodicals, Inc.
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              Multiwfn: a multifunctional wavefunction analyzer.

              Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com. Copyright © 2011 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                Journal
                Analytical Chemistry
                Anal. Chem.
                American Chemical Society (ACS)
                0003-2700
                1520-6882
                November 08 2022
                October 24 2022
                November 08 2022
                : 94
                : 44
                : 15231-15239
                Affiliations
                [1 ]State Key Laboratory of Chemo/Biosensing and Chemometrics, School of Biomedical Sciences, Hunan University, Changsha 410082, P. R. China
                [2 ]College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, P. R. China
                [3 ]College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, P. R. China
                Article
                10.1021/acs.analchem.2c02388
                697d764d-6577-4ad7-bb60-0994bd8c99ae
                © 2022

                https://doi.org/10.15223/policy-029

                https://doi.org/10.15223/policy-037

                https://doi.org/10.15223/policy-045

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