Literature DB >> 28710774

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.

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

Abstract

UCSF ChimeraX is next-generation software for the visualization and analysis of molecular structures, density maps, 3D microscopy, and associated data. It addresses challenges in the size, scope, and disparate types of data attendant with cutting-edge experimental methods, while providing advanced options for high-quality rendering (interactive ambient occlusion, reliable molecular surface calculations, etc.) and professional approaches to software design and distribution. This article highlights some specific advances in the areas of visualization and usability, performance, and extensibility. ChimeraX is free for noncommercial use and is available from http://www.rbvi.ucsf.edu/chimerax/ for Windows, Mac, and Linux.
© 2017 The Protein Society.

Keywords:  biomolecular visualization and analysis; density maps; integrative hybrid modeling; interactive molecular graphics; large-scale data; light-sheet microscopy; structural biology; virtual reality

Mesh:

Year:  2017        PMID: 28710774      PMCID: PMC5734306          DOI: 10.1002/pro.3235

Source DB:  PubMed          Journal:  Protein Sci        ISSN: 0961-8368            Impact factor:   6.725


  44 in total

1.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

2.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

3.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

4.  Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.

Authors:  Yi Shi; Javier Fernandez-Martinez; Elina Tjioe; Riccardo Pellarin; Seung Joong Kim; Rosemary Williams; Dina Schneidman-Duhovny; Andrej Sali; Michael P Rout; Brian T Chait
Journal:  Mol Cell Proteomics       Date:  2014-08-26       Impact factor: 5.911

5.  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

6.  BioCatalogue: a universal catalogue of web services for the life sciences.

Authors:  Jiten Bhagat; Franck Tanoh; Eric Nzuobontane; Thomas Laurent; Jerzy Orlowski; Marco Roos; Katy Wolstencroft; Sergejs Aleksejevs; Robert Stevens; Steve Pettifer; Rodrigo Lopez; Carole A Goble
Journal:  Nucleic Acids Res       Date:  2010-05-19       Impact factor: 16.971

7.  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

8.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Authors:  Fabian Sievers; Andreas Wilm; David Dineen; Toby J Gibson; Kevin Karplus; Weizhong Li; Rodrigo Lopez; Hamish McWilliam; Michael Remmert; Johannes Söding; Julie D Thompson; Desmond G Higgins
Journal:  Mol Syst Biol       Date:  2011-10-11       Impact factor: 11.429

9.  Actin-based protrusions of migrating neutrophils are intrinsically lamellar and facilitate direction changes.

Authors:  Lillian K Fritz-Laylin; Megan Riel-Mehan; Bi-Chang Chen; Samuel J Lord; Thomas D Goddard; Thomas E Ferrin; Susan M Nicholson-Dykstra; Henry Higgs; Graham T Johnson; Eric Betzig; R Dyche Mullins
Journal:  Elife       Date:  2017-09-26       Impact factor: 8.140

10.  The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible.

Authors:  Damian Szklarczyk; John H Morris; Helen Cook; Michael Kuhn; Stefan Wyder; Milan Simonovic; Alberto Santos; Nadezhda T Doncheva; Alexander Roth; Peer Bork; Lars J Jensen; Christian von Mering
Journal:  Nucleic Acids Res       Date:  2016-10-18       Impact factor: 16.971

View more
  1003 in total

1.  Atomic Structures of Anthrax Prechannel Bound with Full-Length Lethal and Edema Factors.

Authors:  Kang Zhou; Shiheng Liu; Nathan J Hardenbrook; Yanxiang Cui; Bryan A Krantz; Z Hong Zhou
Journal:  Structure       Date:  2020-06-09       Impact factor: 5.006

2.  Structures of capsid and capsid-associated tegument complex inside the Epstein-Barr virus.

Authors:  Wei Liu; Yanxiang Cui; Caiyan Wang; Zihang Li; Danyang Gong; Xinghong Dai; Guo-Qiang Bi; Ren Sun; Z Hong Zhou
Journal:  Nat Microbiol       Date:  2020-07-27       Impact factor: 17.745

3.  Structural insights into mammalian mitochondrial translation elongation catalyzed by mtEFG1.

Authors:  Eva Kummer; Nenad Ban
Journal:  EMBO J       Date:  2020-06-30       Impact factor: 11.598

4.  Type 9 secretion system structures reveal a new protein transport mechanism.

Authors:  Frédéric Lauber; Justin C Deme; Susan M Lea; Ben C Berks
Journal:  Nature       Date:  2018-11-07       Impact factor: 49.962

5.  Cryo-EM structure of the native butyrylcholinesterase tetramer reveals a dimer of dimers stabilized by a superhelical assembly.

Authors:  Miguel Ricardo Leung; Laura S van Bezouwen; Lawrence M Schopfer; Joel L Sussman; Israel Silman; Oksana Lockridge; Tzviya Zeev-Ben-Mordehai
Journal:  Proc Natl Acad Sci U S A       Date:  2018-12-11       Impact factor: 11.205

Review 6.  What makes a good new therapeutic L-asparaginase?

Authors:  Angela Beckett; David Gervais
Journal:  World J Microbiol Biotechnol       Date:  2019-09-24       Impact factor: 3.312

7.  Observing 3-hydroxyanthranilate-3,4-dioxygenase in action through a crystalline lens.

Authors:  Yifan Wang; Kathy Fange Liu; Yu Yang; Ian Davis; Aimin Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-30       Impact factor: 11.205

8.  Porcine Circovirus 2 Uses a Multitude of Weak Binding Sites To Interact with Heparan Sulfate, and the Interactions Do Not Follow the Symmetry of the Capsid.

Authors:  Sonali Dhindwal; Bryant Avila; Shanshan Feng; Reza Khayat
Journal:  J Virol       Date:  2019-03-05       Impact factor: 5.103

9.  Transferrin receptor binds virus capsid with dynamic motion.

Authors:  Hyunwook Lee; Heather M Callaway; Javier O Cifuente; Carol M Bator; Colin R Parrish; Susan L Hafenstein
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-23       Impact factor: 11.205

10.  Structural basis for the final steps of human 40S ribosome maturation.

Authors:  Michael Ameismeier; Ivo Zemp; Jasmin van den Heuvel; Matthias Thoms; Otto Berninghausen; Ulrike Kutay; Roland Beckmann
Journal:  Nature       Date:  2020-11-18       Impact factor: 49.962

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.