Literature DB >> 27572735

Databases and Archiving for CryoEM.

A Patwardhan1, C L Lawson2.   

Abstract

CryoEM in structural biology is currently served by three public archives-EMDB for 3DEM reconstructions, PDB for models built from 3DEM reconstructions, and EMPIAR for the raw 2D image data used to obtain the 3DEM reconstructions. These archives play a vital role for both the structural community and the wider biological community in making the data accessible so that results may be reused, reassessed, and integrated with other structural and bioinformatics resources. The important role of the archives is underpinned by the fact that many journals mandate the deposition of data to PDB and EMDB on publication. The field is currently undergoing transformative changes where on the one hand high-resolution structures are becoming a routine occurrence while on the other hand electron tomography is enabling the study of macromolecules in the cellular context. Concomitantly the archives are evolving to best serve their stakeholder communities. In this chapter, we describe the current state of the archives, resources available for depositing, accessing, searching, visualizing and validating data, on-going community-wide initiatives and opportunities, and challenges for the future.
© 2016 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Databases; EMDB; EMDataBank; EMPIAR; Protein Data Bank; Validation

Mesh:

Substances:

Year:  2016        PMID: 27572735      PMCID: PMC5351295          DOI: 10.1016/bs.mie.2016.04.015

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  48 in total

1.  The Protein Data Bank at 40: reflecting on the past to prepare for the future.

Authors:  Helen M Berman; Gerard J Kleywegt; Haruki Nakamura; John L Markley
Journal:  Structure       Date:  2012-03-07       Impact factor: 5.006

2.  Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy.

Authors:  Peter B Rosenthal; Richard Henderson
Journal:  J Mol Biol       Date:  2003-10-31       Impact factor: 5.469

3.  The difficulty of a fair comparison.

Authors: 
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

4.  Recommendations of the wwPDB NMR Validation Task Force.

Authors:  Gaetano T Montelione; Michael Nilges; Ad Bax; Peter Güntert; Torsten Herrmann; Jane S Richardson; Charles D Schwieters; Wim F Vranken; Geerten W Vuister; David S Wishart; Helen M Berman; Gerard J Kleywegt; John L Markley
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

5.  Features and development of Coot.

Authors:  P Emsley; B Lohkamp; W G Scott; K Cowtan
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

6.  Outcome of the first electron microscopy validation task force meeting.

Authors:  Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

7.  Web-based visualisation and analysis of 3D electron-microscopy data from EMDB and PDB.

Authors:  Ingvar Lagerstedt; William J Moore; Ardan Patwardhan; Eduardo Sanz-García; Christoph Best; Jason R Swedlow; Gerard J Kleywegt
Journal:  J Struct Biol       Date:  2013-10-07       Impact factor: 2.867

8.  CTF Challenge: Result summary.

Authors:  Roberto Marabini; Bridget Carragher; Shaoxia Chen; James Chen; Anchi Cheng; Kenneth H Downing; Joachim Frank; Robert A Grassucci; J Bernard Heymann; Wen Jiang; Slavica Jonic; Hstau Y Liao; Steven J Ludtke; Shail Patwari; Angela L Piotrowski; Adrian Quintana; Carlos O S Sorzano; Henning Stahlberg; Javier Vargas; Neil R Voss; Wah Chiu; Jose M Carazo
Journal:  J Struct Biol       Date:  2015-04-23       Impact factor: 2.867

9.  A 3D cellular context for the macromolecular world.

Authors:  Ardan Patwardhan; Alun Ashton; Robert Brandt; Sarah Butcher; Raffaella Carzaniga; Wah Chiu; Lucy Collinson; Pascal Doux; Elizabeth Duke; Mark H Ellisman; Erik Franken; Kay Grünewald; Jean-Karim Heriche; Abraham Koster; Werner Kühlbrandt; Ingvar Lagerstedt; Carolyn Larabell; Catherine L Lawson; Helen R Saibil; Eduardo Sanz-García; Sriram Subramaniam; Paul Verkade; Jason R Swedlow; Gerard J Kleywegt
Journal:  Nat Struct Mol Biol       Date:  2014-10       Impact factor: 15.369

10.  Cryo-EM single particle analysis with the Volta phase plate.

Authors:  Radostin Danev; Wolfgang Baumeister
Journal:  Elife       Date:  2016-03-07       Impact factor: 8.140

View more
  15 in total

1.  Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules.

Authors:  Brinda Vallat; Benjamin Webb; John D Westbrook; Andrej Sali; Helen M Berman
Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

2.  Multi-body Refinement of Cryo-EM Images in RELION.

Authors:  Takanori Nakane; Sjors H W Scheres
Journal:  Methods Mol Biol       Date:  2021

3.  Reducing cryoEM file storage using lossy image formats.

Authors:  Edward T Eng; Mykhailo Kopylov; Carl J Negro; Sarkis Dallaykan; William J Rice; Kelsey D Jordan; Kotaro Kelley; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2019-05-21       Impact factor: 2.867

4.  EMDB Web Resources.

Authors:  Sanja Abbott; Andrii Iudin; Paul K Korir; Sriram Somasundharam; Ardan Patwardhan
Journal:  Curr Protoc Bioinformatics       Date:  2018-04-09

Review 5.  Big data in cryoEM: automated collection, processing and accessibility of EM data.

Authors:  Philip R Baldwin; Yong Zi Tan; Edward T Eng; William J Rice; Alex J Noble; Carl J Negro; Michael A Cianfrocco; Clinton S Potter; Bridget Carragher
Journal:  Curr Opin Microbiol       Date:  2017-10-31       Impact factor: 7.934

Review 6.  Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application.

Authors:  Giovanna Scapin; Clinton S Potter; Bridget Carragher
Journal:  Cell Chem Biol       Date:  2018-08-09       Impact factor: 8.116

Review 7.  From integrative structural biology to cell biology.

Authors:  Andrej Sali
Journal:  J Biol Chem       Date:  2021-05-03       Impact factor: 5.157

8.  Trends in the Electron Microscopy Data Bank (EMDB).

Authors:  Ardan Patwardhan
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-04-20       Impact factor: 7.652

9.  Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.

Authors:  Helen M Berman; Paul D Adams; Alexandre A Bonvin; Stephen K Burley; Bridget Carragher; Wah Chiu; Frank DiMaio; Thomas E Ferrin; Margaret J Gabanyi; Thomas D Goddard; Patrick R Griffin; Juergen Haas; Christian A Hanke; Jeffrey C Hoch; Gerhard Hummer; Genji Kurisu; Catherine L Lawson; Alexander Leitner; John L Markley; Jens Meiler; Gaetano T Montelione; George N Phillips; Thomas Prisner; Juri Rappsilber; David C Schriemer; Torsten Schwede; Claus A M Seidel; Timothy S Strutzenberg; Dmitri I Svergun; Emad Tajkhorshid; Jill Trewhella; Brinda Vallat; Sameer Velankar; Geerten W Vuister; Benjamin Webb; John D Westbrook; Kate L White; Andrej Sali
Journal:  Structure       Date:  2019-11-25       Impact factor: 5.006

10.  Reporting on the future of integrative structural biology ORAU workshop.

Authors:  George L Hamilton; Joshua Alper; Hugo Sanabria
Journal:  Front Biosci (Landmark Ed)       Date:  2020-01-01
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.