Literature DB >> 26935210

The impact of structural genomics: the first quindecennial.

Marek Grabowski1, Ewa Niedzialkowska1,2, Matthew D Zimmerman1, Wladek Minor3.   

Abstract

The period 2000-2015 brought the advent of high-throughput approaches to protein structure determination. With the overall funding on the order of $2 billion (in 2010 dollars), the structural genomics (SG) consortia established worldwide have developed pipelines for target selection, protein production, sample preparation, crystallization, and structure determination by X-ray crystallography and NMR. These efforts resulted in the determination of over 13,500 protein structures, mostly from unique protein families, and increased the structural coverage of the expanding protein universe. SG programs contributed over 4400 publications to the scientific literature. The NIH-funded Protein Structure Initiatives alone have produced over 2000 scientific publications, which to date have attracted more than 93,000 citations. Software and database developments that were necessary to handle high-throughput structure determination workflows have led to structures of better quality and improved integrity of the associated data. Organized and accessible data have a positive impact on the reproducibility of scientific experiments. Most of the experimental data generated by the SG centers are freely available to the community and has been utilized by scientists in various fields of research. SG projects have created, improved, streamlined, and validated many protocols for protein production and crystallization, data collection, and functional analysis, significantly benefiting biological and biomedical research.

Entities:  

Keywords:  NMR; Protein crystallography; Structural genomics

Mesh:

Substances:

Year:  2016        PMID: 26935210      PMCID: PMC4834271          DOI: 10.1007/s10969-016-9201-5

Source DB:  PubMed          Journal:  J Struct Funct Genomics        ISSN: 1345-711X


  86 in total

Review 1.  Protein expression systems for structural genomics and proteomics.

Authors:  Shigeyuki Yokoyama
Journal:  Curr Opin Chem Biol       Date:  2003-02       Impact factor: 8.822

2.  What is missing from descriptions of treatment in trials and reviews?

Authors:  Paul Glasziou; Emma Meats; Carl Heneghan; Sasha Shepperd
Journal:  BMJ       Date:  2008-06-28

3.  Broad-substrate screen as a tool to identify substrates for bacterial Gcn5-related N-acetyltransferases with unknown substrate specificity.

Authors:  Misty L Kuhn; Karolina A Majorek; Wladek Minor; Wayne F Anderson
Journal:  Protein Sci       Date:  2012-12-17       Impact factor: 6.725

Review 4.  Unmet challenges of structural genomics.

Authors:  Maksymilian Chruszcz; Marcin Domagalski; Tomasz Osinski; Alexander Wlodawer; Wladek Minor
Journal:  Curr Opin Struct Biol       Date:  2010-08-31       Impact factor: 6.809

5.  An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database.

Authors:  Naohiro Kobayashi; Yoko Harano; Naoya Tochio; Eiichi Nakatani; Takanori Kigawa; Shigeyuki Yokoyama; Steve Mading; Eldon L Ulrich; John L Markley; Hideo Akutsu; Toshimichi Fujiwara
Journal:  J Biomol NMR       Date:  2012-06-13       Impact factor: 2.835

6.  Identification of unknown protein function using metabolite cocktail screening.

Authors:  Igor A Shumilin; Marcin Cymborowski; Olga Chertihin; Kula N Jha; John C Herr; Scott A Lesley; Andrzej Joachimiak; Wladek Minor
Journal:  Structure       Date:  2012-08-30       Impact factor: 5.006

7.  The Protein Information Management System (PiMS): a generic tool for any structural biology research laboratory.

Authors:  Chris Morris; Anne Pajon; Susanne L Griffiths; Ed Daniel; Marc Savitsky; Bill Lin; Jonathan M Diprose; Alan Wilter da Silva; Katya Pilicheva; Peter Troshin; Johannes van Niekerk; Neil Isaacs; James Naismith; Colin Nave; Richard Blake; Keith S Wilson; David I Stuart; Kim Henrick; Robert M Esnouf
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

8.  The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

Authors:  Margaret J Gabanyi; Paul D Adams; Konstantin Arnold; Lorenza Bordoli; Lester G Carter; Judith Flippen-Andersen; Lida Gifford; Juergen Haas; Andrei Kouranov; William A McLaughlin; David I Micallef; Wladek Minor; Raship Shah; Torsten Schwede; Yi-Ping Tao; John D Westbrook; Matthew Zimmerman; Helen M Berman
Journal:  J Struct Funct Genomics       Date:  2011-04-07

Review 9.  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

10.  DNASU plasmid and PSI:Biology-Materials repositories: resources to accelerate biological research.

Authors:  Catherine Y Seiler; Jin G Park; Amit Sharma; Preston Hunter; Padmini Surapaneni; Casey Sedillo; James Field; Rhys Algar; Andrea Price; Jason Steel; Andrea Throop; Michael Fiacco; Joshua LaBaer
Journal:  Nucleic Acids Res       Date:  2013-11-12       Impact factor: 16.971

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  24 in total

Review 1.  Critical evaluation of bioinformatics tools for the prediction of protein crystallization propensity.

Authors:  Huilin Wang; Liubin Feng; Geoffrey I Webb; Lukasz Kurgan; Jiangning Song; Donghai Lin
Journal:  Brief Bioinform       Date:  2018-09-28       Impact factor: 11.622

Review 2.  Protein-RNA interactions: structural biology and computational modeling techniques.

Authors:  Susan Jones
Journal:  Biophys Rev       Date:  2016-11-14

Review 3.  Serial Crystallography for Structure-Based Drug Discovery.

Authors:  Lan Zhu; Xiaoyu Chen; Enrique E Abola; Liang Jing; Wei Liu
Journal:  Trends Pharmacol Sci       Date:  2020-09-16       Impact factor: 14.819

4.  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 5.  Anticipating innovations in structural biology.

Authors:  Helen M Berman; Catherine L Lawson; Brinda Vallat; Margaret J Gabanyi
Journal:  Q Rev Biophys       Date:  2018-01       Impact factor: 5.318

Review 6.  Signaling through non-membrane nuclear phosphoinositide binding proteins in human health and disease.

Authors:  Jamal M Bryant; Raymond D Blind
Journal:  J Lipid Res       Date:  2018-09-10       Impact factor: 5.922

Review 7.  The young person's guide to the PDB.

Authors:  Wladek Minor; Zbigniew Dauter; Mariusz Jaskolski
Journal:  Postepy Biochem       Date:  2016

8.  Synchrotron Radiation as a Tool for Macromolecular X-Ray Crystallography: a XXI Century Perspective.

Authors:  Marek Grabowski; David R Cooper; Dariusz Brzezinski; Joanna M Macnar; Ivan G Shabalin; Marcin Cymborowski; Zbyszek Otwinowski; Wladek Minor
Journal:  Nucl Instrum Methods Phys Res B       Date:  2021-01-05       Impact factor: 1.377

9.  ProtCHOIR: a tool for proteome-scale generation of homo-oligomers.

Authors:  Pedro H M Torres; Artur D Rossi; Tom L Blundell
Journal:  Brief Bioinform       Date:  2021-11-05       Impact factor: 11.622

Review 10.  Residue-based pharmacophore approaches to study protein-protein interactions.

Authors:  Rojan Shrestha; Jorge Eduardo Fajardo; Andras Fiser
Journal:  Curr Opin Struct Biol       Date:  2021-01-22       Impact factor: 6.809

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