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UCSF ChimeraX:面向研究人员、教育工作者和开发者的结构可视化工具。

UCSF ChimeraX: Structure visualization for researchers, educators, and developers.

机构信息

Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, USA.

Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Cambridge, UK.

出版信息

Protein Sci. 2021 Jan;30(1):70-82. doi: 10.1002/pro.3943. Epub 2020 Oct 22.

Abstract

UCSF ChimeraX is the next-generation interactive visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera. ChimeraX brings (a) significant performance and graphics enhancements; (b) new implementations of Chimera's most highly used tools, many with further improvements; (c) several entirely new analysis features; (d) support for new areas such as virtual reality, light-sheet microscopy, and medical imaging data; (e) major ease-of-use advances, including toolbars with icons to perform actions with a single click, basic "undo" capabilities, and more logical and consistent commands; and (f) an app store for researchers to contribute new tools. ChimeraX includes full user documentation and is free for noncommercial use, with downloads available for Windows, Linux, and macOS from https://www.rbvi.ucsf.edu/chimerax.

摘要

UCSF ChimeraX 是下一代交互式可视化程序,由生物计算、可视化和信息学资源(RBVI)开发,是 UCSF Chimera 的后续产品。ChimeraX 带来了:(a) 显著的性能和图形增强;(b) Chimera 最常用工具的新实现,其中许多工具都有进一步的改进;(c) 几个全新的分析功能;(d) 对虚拟现实、光片显微镜和医学成像数据等新领域的支持;(e) 主要的易用性改进,包括带有图标的工具栏,可通过单击执行操作,基本的“撤消”功能,以及更合理和一致的命令;以及 (f) 一个应用程序商店,供研究人员贡献新工具。ChimeraX 包括完整的用户文档,可免费用于非商业用途,可从 https://www.rbvi.ucsf.edu/chimerax 下载适用于 Windows、Linux 和 macOS 的版本。

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本文引用的文献

1
Single-particle cryo-EM at atomic resolution.
Nature. 2020 Nov;587(7832):152-156. doi: 10.1038/s41586-020-2829-0. Epub 2020 Oct 21.
2
Structural Basis for Potent Neutralization of Betacoronaviruses by Single-Domain Camelid Antibodies.
Cell. 2020 May 28;181(5):1004-1015.e15. doi: 10.1016/j.cell.2020.04.031. Epub 2020 May 5.
4
Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.
Science. 2020 Mar 13;367(6483):1260-1263. doi: 10.1126/science.abb2507. Epub 2020 Feb 19.
5
Dense connectomic reconstruction in layer 4 of the somatosensory cortex.
Science. 2019 Nov 29;366(6469). doi: 10.1126/science.aay3134. Epub 2019 Oct 24.
6
UniProt: a worldwide hub of protein knowledge.
Nucleic Acids Res. 2019 Jan 8;47(D1):D506-D515. doi: 10.1093/nar/gky1049.
7
EMDB Web Resources.
Curr Protoc Bioinformatics. 2018 Mar;61(1):5.10.1-5.10.12. doi: 10.1002/cpbi.48. Epub 2018 Apr 9.
8
Molecular Visualization on the Holodeck.
J Mol Biol. 2018 Oct 19;430(21):3982-3996. doi: 10.1016/j.jmb.2018.06.040. Epub 2018 Jun 28.
9
ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Acta Crystallogr D Struct Biol. 2018 Jun 1;74(Pt 6):519-530. doi: 10.1107/S2059798318002425. Epub 2018 Apr 11.
10
Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.
Structure. 2018 Jun 5;26(6):894-904.e2. doi: 10.1016/j.str.2018.03.011. Epub 2018 Apr 12.

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