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Literature DB >> 32881101

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

Eric F Pettersen¹, Thomas D Goddard¹, Conrad C Huang¹, Elaine C Meng¹, Gregory S Couch¹, Tristan I Croll², John H Morris¹, Thomas E Ferrin¹.

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.

Entities: Chemical

Keywords: cryoEM; density maps; interactive visualization and analysis; molecular graphics; molecular modeling; structural biology; virtual reality

Mesh：

Year: 2020 PMID： 32881101 PMCID： PMC7737788 DOI： 10.1002/pro.3943

Source DB: PubMed Journal: Protein Sci ISSN： 0961-8368 Impact factor: 6.993

33 in total

1. The Protein Data Bank.

Authors: H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal: Nucleic Acids Res Date: 2000-01-01 Impact factor: 16.971

2. UCSF Chimera--a visualization system for exploratory research and analysis.

Authors: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin
Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376

3. Cryo-EM of macromolecular assemblies at near-atomic resolution.

Authors: Matthew L Baker; Junjie Zhang; Steven J Ludtke; Wah Chiu
Journal: Nat Protoc Date: 2010-09-30 Impact factor: 13.491

4. Web services at the European Bioinformatics Institute-2009.

Authors: Hamish McWilliam; Franck Valentin; Mickael Goujon; Weizhong Li; Menaka Narayanasamy; Jenny Martin; Teresa Miyar; Rodrigo Lopez
Journal: Nucleic Acids Res Date: 2009-05-12 Impact factor: 16.971

5. ModBase, a database of annotated comparative protein structure models, and associated resources.

Authors: Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
Journal: Nucleic Acids Res Date: 2010-11-19 Impact factor: 16.971

6. Enhancing UCSF Chimera through web services.

Authors: Conrad C Huang; Elaine C Meng; John H Morris; Eric F Pettersen; Thomas E Ferrin
Journal: Nucleic Acids Res Date: 2014-05-26 Impact factor: 16.971

7. UniProt: a worldwide hub of protein knowledge.

Authors:
Journal: Nucleic Acids Res Date: 2019-01-08 Impact factor: 16.971

8. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation.

Authors: Daniel Wrapp; Nianshuang Wang; Kizzmekia S Corbett; Jory A Goldsmith; Ching-Lin Hsieh; Olubukola Abiona; Barney S Graham; Jason S McLellan
Journal: Science Date: 2020-02-19 Impact factor: 47.728

9. Cytoscape app store.

Authors: Samad Lotia; Jason Montojo; Yue Dong; Gary D Bader; Alexander R Pico
Journal: Bioinformatics Date: 2013-04-16 Impact factor: 6.937

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

Authors: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Elaine C Meng; Gregory S Couch; Tristan I Croll; John H Morris; Thomas E Ferrin
Journal: Protein Sci Date: 2020-10-22 Impact factor: 6.993

675 in total

1. Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel.

Authors: Pramod Kumar; Gisela D Cymes; Claudio Grosman
Journal: Proc Natl Acad Sci U S A Date: 2021-06-08 Impact factor: 11.205

2. Structural insights into the human D1 and D2 dopamine receptor signaling complexes.

Authors: Youwen Zhuang; Peiyu Xu; Chunyou Mao; Lei Wang; Brian Krumm; X Edward Zhou; Sijie Huang; Heng Liu; Xi Cheng; Xi-Ping Huang; Dan-Dan Shen; Tinghai Xu; Yong-Feng Liu; Yue Wang; Jia Guo; Yi Jiang; Hualiang Jiang; Karsten Melcher; Bryan L Roth; Yan Zhang; Cheng Zhang; H Eric Xu
Journal: Cell Date: 2021-02-10 Impact factor: 41.582

3. CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes.

Authors: Meghna Gupta; Caleigh M Azumaya; Michelle Moritz; Sergei Pourmal; Amy Diallo; Gregory E Merz; Gwendolyn Jang; Mehdi Bouhaddou; Andrea Fossati; Axel F Brilot; Devan Diwanji; Evelyn Hernandez; Nadia Herrera; Huong T Kratochvil; Victor L Lam; Fei Li; Yang Li; Henry C Nguyen; Carlos Nowotny; Tristan W Owens; Jessica K Peters; Alexandrea N Rizo; Ursula Schulze-Gahmen; Amber M Smith; Iris D Young; Zanlin Yu; Daniel Asarnow; Christian Billesbølle; Melody G Campbell; Jen Chen; Kuei-Ho Chen; Un Seng Chio; Miles Sasha Dickinson; Loan Doan; Mingliang Jin; Kate Kim; Junrui Li; Yen-Li Li; Edmond Linossi; Yanxin Liu; Megan Lo; Jocelyne Lopez; Kyle E Lopez; Adamo Mancino; Frank R Moss; Michael D Paul; Komal Ishwar Pawar; Adrian Pelin; Thomas H Pospiech; Cristina Puchades; Soumya Govinda Remesh; Maliheh Safari; Kaitlin Schaefer; Ming Sun; Mariano C Tabios; Aye C Thwin; Erron W Titus; Raphael Trenker; Eric Tse; Tsz Kin Martin Tsui; Feng Wang; Kaihua Zhang; Yang Zhang; Jianhua Zhao; Fengbo Zhou; Yuan Zhou; Lorena Zuliani-Alvarez; David A Agard; Yifan Cheng; James S Fraser; Natalia Jura; Tanja Kortemme; Aashish Manglik; Daniel R Southworth; Robert M Stroud; Danielle L Swaney; Nevan J Krogan; Adam Frost; Oren S Rosenberg; Kliment A Verba
Journal: bioRxiv Date: 2021-05-11

4. Mechanosensitive channel gating by delipidation.

Authors: Vanessa Judith Flegler; Akiko Rasmussen; Karina Borbil; Lea Boten; Hsuan-Ai Chen; Hanna Deinlein; Julia Halang; Kristin Hellmanzik; Jessica Löffler; Vanessa Schmidt; Cihan Makbul; Christian Kraft; Rainer Hedrich; Tim Rasmussen; Bettina Böttcher
Journal: Proc Natl Acad Sci U S A Date: 2021-08-17 Impact factor: 11.205

5. Structural insights into ligand recognition and activation of the melanocortin-4 receptor.

Authors: Huibing Zhang; Li-Nan Chen; Dehua Yang; Chunyou Mao; Qingya Shen; Wenbo Feng; Dan-Dan Shen; Antao Dai; Shanshan Xie; Yan Zhou; Jiao Qin; Jin-Peng Sun; Daniel H Scharf; Tingjun Hou; Tianhua Zhou; Ming-Wei Wang; Yan Zhang
Journal: Cell Res Date: 2021-08-25 Impact factor: 25.617

6. A Non-covalent Ligand Reveals Biased Agonism of the TRPA1 Ion Channel.

Authors: Chang Liu; Rebecca Reese; Simon Vu; Lionel Rougé; Shannon D Shields; Satoko Kakiuchi-Kiyota; Huifen Chen; Kevin Johnson; Yu Patrick Shi; Tania Chernov-Rogan; Demi Maria Zabala Greiner; Pawan Bir Kohli; David Hackos; Bobby Brillantes; Christine Tam; Tianbo Li; Jianyong Wang; Brian Safina; Steve Magnuson; Matthew Volgraf; Jian Payandeh; Jie Zheng; Alexis Rohou; Jun Chen
Journal: Neuron Date: 2020-11-04 Impact factor: 17.173

7. Structural insights into the lipid and ligand regulation of serotonin receptors.

Authors: Peiyu Xu; Sijie Huang; Huibing Zhang; Chunyou Mao; X Edward Zhou; Xi Cheng; Icaro A Simon; Dan-Dan Shen; Hsin-Yung Yen; Carol V Robinson; Kasper Harpsøe; Bo Svensson; Jia Guo; Hualiang Jiang; David E Gloriam; Karsten Melcher; Yi Jiang; Yan Zhang; H Eric Xu
Journal: Nature Date: 2021-03-24 Impact factor: 49.962

8. DNA interference states of the hypercompact CRISPR-CasΦ effector.

Authors: Patrick Pausch; Katarzyna M Soczek; Dominik A Herbst; Connor A Tsuchida; Basem Al-Shayeb; Jillian F Banfield; Eva Nogales; Jennifer A Doudna
Journal: Nat Struct Mol Biol Date: 2021-08-11 Impact factor: 15.369

Review 9. Drug discovery in the era of cryo-electron microscopy.

Authors: Michael J Robertson; Justin G Meyerowitz; Georgios Skiniotis
Journal: Trends Biochem Sci Date: 2021-07-16 Impact factor: 13.807

10. Structural mechanism of heat-induced opening of a temperature-sensitive TRP channel.

Authors: Kirill D Nadezhdin; Arthur Neuberger; Yuri A Trofimov; Nikolay A Krylov; Viktor Sinica; Nikita Kupko; Viktorie Vlachova; Eleonora Zakharian; Roman G Efremov; Alexander I Sobolevsky
Journal: Nat Struct Mol Biol Date: 2021-07-08 Impact factor: 15.369