Literature DB >> 20810277

Unmet challenges of structural genomics.

Maksymilian Chruszcz1, Marcin Domagalski, Tomasz Osinski, Alexander Wlodawer, Wladek Minor.   

Abstract

Structural genomics (SG) programs have developed during the last decade many novel methodologies for faster and more accurate structure determination. These new tools and approaches led to the determination of thousands of protein structures. The generation of enormous amounts of experimental data resulted in significant improvements in the understanding of many biological processes at molecular levels. However, the amount of data collected so far is so large that traditional analysis methods are limiting the rate of extraction of biological and biochemical information from 3D models. This situation has prompted us to review the challenges that remain unmet by SG, as well as the areas in which the potential impact of SG could exceed what has been achieved so far.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2010        PMID: 20810277      PMCID: PMC3017768          DOI: 10.1016/j.sbi.2010.08.001

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  79 in total

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Review 2.  Structural genomics-impact on biomedicine and drug discovery.

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Journal:  Exp Cell Res       Date:  2010-03-06       Impact factor: 3.905

Review 3.  X-ray diffraction experiment--the last experiment in the structure elucidation process.

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4.  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

Review 5.  Structural genomics and drug discovery for infectious diseases.

Authors:  W F Anderson
Journal:  Infect Disord Drug Targets       Date:  2009-11

Review 6.  Engineering of recombinant crystallization chaperones.

Authors:  Shohei Koide
Journal:  Curr Opin Struct Biol       Date:  2009-05-26       Impact factor: 6.809

7.  Proteopedia - a scientific 'wiki' bridging the rift between three-dimensional structure and function of biomacromolecules.

Authors:  Eran Hodis; Jaime Prilusky; Eric Martz; Israel Silman; John Moult; Joel L Sussman
Journal:  Genome Biol       Date:  2008-08-03       Impact factor: 13.583

Review 8.  SPINE bioinformatics and data-management aspects of high-throughput structural biology.

Authors:  S Albeck; P Alzari; C Andreini; L Banci; I M Berry; I Bertini; C Cambillau; B Canard; L Carter; S X Cohen; J M Diprose; O Dym; R M Esnouf; C Felder; F Ferron; F Guillemot; R Hamer; M Ben Jelloul; R A Laskowski; T Laurent; S Longhi; R Lopez; C Luchinat; H Malet; T Mochel; R J Morris; L Moulinier; T Oinn; A Pajon; Y Peleg; A Perrakis; O Poch; J Prilusky; A Rachedi; R Ripp; A Rosato; I Silman; D I Stuart; J L Sussman; J C Thierry; J D Thompson; J M Thornton; T Unger; B Vaughan; W Vranken; J D Watson; G Whamond; K Henrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2006-09-19

9.  Re-refinement from deposited X-ray data can deliver improved models for most PDB entries.

Authors:  Robbie P Joosten; Thomas Womack; Gert Vriend; Gérard Bricogne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20

10.  In situ proteolysis to generate crystals for structure determination: an update.

Authors:  Amy Wernimont; Aled Edwards
Journal:  PLoS One       Date:  2009-04-07       Impact factor: 3.240

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  27 in total

1.  The quality and validation of structures from structural genomics.

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Review 2.  X-ray crystallography over the past decade for novel drug discovery - where are we heading next?

Authors:  Heping Zheng; Katarzyna B Handing; Matthew D Zimmerman; Ivan G Shabalin; Steven C Almo; Wladek Minor
Journal:  Expert Opin Drug Discov       Date:  2015-07-15       Impact factor: 6.098

3.  Creating a community resource for protein science.

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

4.  Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server.

Authors:  Heping Zheng; Mahendra D Chordia; David R Cooper; Maksymilian Chruszcz; Peter Müller; George M Sheldrick; Wladek Minor
Journal:  Nat Protoc       Date:  2013-12-19       Impact factor: 13.491

5.  A new approach to assess and predict the functional roles of proteins across all known structures.

Authors:  Elchin S Julfayev; Ryan J McLaughlin; Yi-Ping Tao; William A McLaughlin
Journal:  J Struct Funct Genomics       Date:  2011-03-29

6.  Molstack-Interactive visualization tool for presentation, interpretation, and validation of macromolecules and electron density maps.

Authors:  Przemyslaw J Porebski; Piotr Sroka; Heping Zheng; David R Cooper; Wladek Minor
Journal:  Protein Sci       Date:  2017-09-13       Impact factor: 6.725

Review 7.  Databases, Repositories, and Other Data Resources in Structural Biology.

Authors:  Heping Zheng; Przemyslaw J Porebski; Marek Grabowski; David R Cooper; Wladek Minor
Journal:  Methods Mol Biol       Date:  2017

Review 8.  The impact of structural genomics: the first quindecennial.

Authors:  Marek Grabowski; Ewa Niedzialkowska; Matthew D Zimmerman; Wladek Minor
Journal:  J Struct Funct Genomics       Date:  2016-03-02

9.  Discovering RNA-protein interactome by using chemical context profiling of the RNA-protein interface.

Authors:  Marc Parisien; Xiaoyun Wang; George Perdrizet; Corissa Lamphear; Carol A Fierke; Ketan C Maheshwari; Michael J Wilde; Tobin R Sosnick; Tao Pan
Journal:  Cell Rep       Date:  2013-05-09       Impact factor: 9.423

Review 10.  Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

Authors:  Alexander Wlodawer; Wladek Minor; Zbigniew Dauter; Mariusz Jaskolski
Journal:  FEBS J       Date:  2013-09-18       Impact factor: 5.542

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