EMDataBank unified data resource for 3DEM

Catherine L Lawson; Ardan Patwardhan; Matthew L Baker; Corey Hryc; Eduardo Sanz Garcia; Brian P Hudson; Ingvar Lagerstedt; Steven J Ludtke; Grigore Pintilie; Raul Sala; John D Westbrook; Helen M Berman; Gerard J Kleywegt; Wah Chiu

doi:10.1093/nar/gkv1126

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EMDataBank unified data resource for 3DEM

Journal article

Open access

Peer reviewed

EMDataBank unified data resource for 3DEM

Catherine L Lawson, Ardan Patwardhan, Matthew L Baker, Corey Hryc, Eduardo Sanz Garcia, Brian P Hudson, Ingvar Lagerstedt, Steven J Ludtke, Grigore Pintilie, Raul Sala, …

Nucleic acids research, Vol.44(D1), pp.D396-D403

01/04/2016

DOI: https://doi.org/10.1093/nar/gkv1126

PMCID: PMC4702818

PMID: 26578576

Abstract

Databases, Factual

Databases, Protein

Imaging, Three-Dimensional

Macromolecular Substances - chemistry

Microscopy, Electron

Models, Molecular

Proteins - chemistry

Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataBank project provides a unified portal for deposition, retrieval and analysis of 3DEM density maps, atomic models and associated metadata (emdatabank.org). We provide here an overview of the rapidly growing 3DEM structural data archives, which include maps in EM Data Bank and map-derived models in the Protein Data Bank. In addition, we describe progress and approaches toward development of validation protocols and methods, working with the scientific community, in order to create a validation pipeline for 3DEM data.

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Title: EMDataBank unified data resource for 3DEM
Creators: Catherine L Lawson - Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA cathy.lawson@rutgers.edu
Ardan Patwardhan - Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK ardan@ebi.ac.uk
Matthew L Baker - Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
Corey Hryc - Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
Eduardo Sanz Garcia - Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Brian P Hudson - Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
Ingvar Lagerstedt - Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Steven J Ludtke - Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
Grigore Pintilie - Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA
Raul Sala - Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
John D Westbrook - Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
Helen M Berman - Department of Chemistry and Chemical Biology and Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, 610 Taylor Road Piscataway, NJ 08854, USA
Gerard J Kleywegt - Protein Data Bank in Europe, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
Wah Chiu - Verna and Marrs McLean Department of Biochemistry & Molecular Biology, National Center for Macromolecular Imaging, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 70030, USA wah@bcm.edu
Publication Details: Nucleic acids research, Vol.44(D1), pp.D396-D403
Date published: 01/04/2016
Grant note: MR/L007835/1 / Medical Research Council BB/G022577/1 / Biotechnology and Biological Sciences Research Council P41 GM103832 / NIGMS NIH HHS MR/L007835 / Medical Research Council R01GM079429 / NIGMS NIH HHS 088944 / Wellcome Trust 104948 / Wellcome Trust R01 GM079429 / NIGMS NIH HHS
Academic Unit: Chemistry and Chemical Biology (SAS); Institute for Quantitative Biomedicine
Language: English
Resource Type: Journal article
Identifiers: 991031666179404646