Literature DB >> 10089486

Deposition of macromolecular structures.

P A Keller1, K Henrick, P McNeil, S Moodie, G J Barton.   

Abstract

Macromolecular structures are being determined at an increasing rate, and are of interest to a wide diversity of researchers. Depositing a macromolecular structure with the Protein Data Bank makes it readily available to the community. Accuracy, consistency and machine-readability of the data are essential, as are clear indications of quality, and sufficient information to allow non-experimentalists to interpret the data. Good-quality depositions are necessary to allow this to be achieved. The PDB's AutoDep system allows deposition and some preliminary automatic checking to take place at multiple sites, prior to full processing and release of the structure by the PDB. However, depositing a structure currently requires the manual entry of a large amount of information at the time of deposition. The data-harvesting approach will allow much more information to be deposited, without placing an additional burden on the depositor. Deposition-ready files will be generated automatically during the course of a structure-determination experiment. The additional information will allow improved validation procedures to be applied to the structures, and the data to be made more useful to the wider scientific community.

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Mesh:

Year:  1998        PMID: 10089486     DOI: 10.1107/s0907444998008464

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  8 in total

Review 1.  Bioinformatics methods to predict protein structure and function. A practical approach.

Authors:  Yvonne J K Edwards; Amanda Cottage
Journal:  Mol Biotechnol       Date:  2003-02       Impact factor: 2.695

2.  Modeling shape and topology of low-resolution density maps of biological macromolecules.

Authors:  Pedro A De-Alarcón; Alberto Pascual-Montano; Amarnath Gupta; Jose M Carazo
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

3.  Deposit3D: a tool for automating structure depositions to the Protein Data Bank.

Authors:  J Badger; J Hendle; S K Burley; C R Kissinger
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2005-08-31

4.  The Protein Data Bank Archive.

Authors:  Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2021

5.  Creating a community resource for protein science.

Authors:  Helen M Berman
Journal:  Protein Sci       Date:  2012-09-28       Impact factor: 6.725

Review 6.  Protein Data Bank (PDB): The Single Global Macromolecular Structure Archive.

Authors:  Stephen K Burley; Helen M Berman; Gerard J Kleywegt; John L Markley; Haruki Nakamura; Sameer Velankar
Journal:  Methods Mol Biol       Date:  2017

Review 7.  Trendspotting in the Protein Data Bank.

Authors:  Helen M Berman; Buvaneswari Coimbatore Narayanan; Luigi Di Costanzo; Shuchismita Dutta; Sutapa Ghosh; Brian P Hudson; Catherine L Lawson; Ezra Peisach; Andreas Prlić; Peter W Rose; Chenghua Shao; Huanwang Yang; Jasmine Young; Christine Zardecki
Journal:  FEBS Lett       Date:  2013-01-18       Impact factor: 4.124

8.  Remediation of the protein data bank archive.

Authors:  Kim Henrick; Zukang Feng; Wolfgang F Bluhm; Dimitris Dimitropoulos; Jurgen F Doreleijers; Shuchismita Dutta; Judith L Flippen-Anderson; John Ionides; Chisa Kamada; Eugene Krissinel; Catherine L Lawson; John L Markley; Haruki Nakamura; Richard Newman; Yukiko Shimizu; Jawahar Swaminathan; Sameer Velankar; Jeramia Ory; Eldon L Ulrich; Wim Vranken; John Westbrook; Reiko Yamashita; Huanwang Yang; Jasmine Young; Muhammed Yousufuddin; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2007-12-11       Impact factor: 16.971

  8 in total

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