Literature DB >> 18406627

Software tools for molecular microscopy.

Ross Smith1, Bridget Carragher.   

Abstract

In our role as the editors of a special edition of the Journal of Structural Biology published in 1996 and devoted to the development of software tools, we offer our view of past developments and future prospects in this area. The astonishing progress in computer hardware over the past decade has fueled a significant increase in computational power available for the solution of macromolecular structures. At the same time the relatively slow growth and development of the accompanying software reflects the difficulties of developing large, complex and very specialized analytical methods.

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Year:  2008        PMID: 18406627      PMCID: PMC2572711          DOI: 10.1016/j.jsb.2008.03.002

Source DB:  PubMed          Journal:  J Struct Biol        ISSN: 1047-8477            Impact factor:   2.867


  25 in total

1.  EMAN: semiautomated software for high-resolution single-particle reconstructions.

Authors:  S J Ludtke; P R Baldwin; W Chiu
Journal:  J Struct Biol       Date:  1999-12-01       Impact factor: 2.867

2.  A relational database for cryoEM: experience at one year and 50 000 images.

Authors:  Denis Fellmann; James Pulokas; Ronald A Milligan; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2002-03       Impact factor: 2.867

3.  The parallelization of SPIDER on distributed-memory computers using MPI.

Authors:  Chao Yang; Pawel A Penczek; ArDean Leith; Francisco J Asturias; Esmond G Ng; Robert M Glaeser; Joachim Frank
Journal:  J Struct Biol       Date:  2006-06-08       Impact factor: 2.867

4.  SPARX, a new environment for Cryo-EM image processing.

Authors:  Michael Hohn; Grant Tang; Grant Goodyear; P R Baldwin; Zhong Huang; Pawel A Penczek; Chao Yang; Robert M Glaeser; Paul D Adams; Steven J Ludtke
Journal:  J Struct Biol       Date:  2006-07-16       Impact factor: 2.867

5.  SPIRE: the SPIDER reconstruction engine.

Authors:  William T Baxter; ArDean Leith; Joachim Frank
Journal:  J Struct Biol       Date:  2006-08-25       Impact factor: 2.867

6.  2dx--user-friendly image processing for 2D crystals.

Authors:  Bryant Gipson; Xiangyan Zeng; Zi Yan Zhang; Henning Stahlberg
Journal:  J Struct Biol       Date:  2006-09-01       Impact factor: 2.867

7.  Integrating electron microscopy information into existing Distributed Annotation Systems.

Authors:  J R Macías; N Jiménez-Lozano; J M Carazo
Journal:  J Struct Biol       Date:  2007-02-24       Impact factor: 2.867

8.  Estimation of variance in single-particle reconstruction using the bootstrap technique.

Authors:  Pawel A Penczek; Chao Yang; Joachim Frank; Christian M T Spahn
Journal:  J Struct Biol       Date:  2006-02-13       Impact factor: 2.867

Review 9.  The micrograph data processing program.

Authors:  P R Smith; S M Gottesman
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

10.  Digital image processing of electron micrographs: the PIC system-III.

Authors:  B L Trus; E Kocsis; J F Conway; A C Steven
Journal:  J Struct Biol       Date:  1996 Jan-Feb       Impact factor: 2.867

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  3 in total

1.  A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.

Authors:  Neil R Voss; Dmitry Lyumkis; Anchi Cheng; Pick-Wei Lau; Anke Mulder; Gabriel C Lander; Edward J Brignole; Denis Fellmann; Christopher Irving; Erica L Jacovetty; Albert Leung; James Pulokas; Joel D Quispe; Hanspeter Winkler; Craig Yoshioka; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2009-12-16       Impact factor: 2.867

2.  Appion: an integrated, database-driven pipeline to facilitate EM image processing.

Authors:  Gabriel C Lander; Scott M Stagg; Neil R Voss; Anchi Cheng; Denis Fellmann; James Pulokas; Craig Yoshioka; Christopher Irving; Anke Mulder; Pick-Wei Lau; Dmitry Lyumkis; Clinton S Potter; Bridget Carragher
Journal:  J Struct Biol       Date:  2009-04       Impact factor: 2.867

3.  Development of basic building blocks for cryo-EM: the emcore and emvis software libraries.

Authors:  José Miguel de la Rosa-Trevín; Pedro Alberto Hernández Viga; Joaquín Otón; Erik Lindahl
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-03-31       Impact factor: 7.652

  3 in total

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