Literature DB >> 19416074

Lessons from structural genomics.

Thomas C Terwilliger1, David Stuart, Shigeyuki Yokoyama.   

Abstract

A decade of structural genomics, the large-scale determination of protein structures, has generated a wealth of data and many important lessons for structural biology and for future large-scale projects. These lessons include a confirmation that it is possible to construct large-scale facilities that can determine the structures of a hundred or more proteins per year, that these structures can be of high quality, and that these structures can have an important impact. Technology development has played a critical role in structural genomics, the difficulties at each step of determining a structure of a particular protein can be quantified, and validation of technologies is nearly as important as the technologies themselves. Finally, rapid deposition of data in public databases has increased the impact and usefulness of the data and international cooperation has advanced the field and improved data sharing.

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Year:  2009        PMID: 19416074      PMCID: PMC2847842          DOI: 10.1146/annurev.biophys.050708.133740

Source DB:  PubMed          Journal:  Annu Rev Biophys        ISSN: 1936-122X            Impact factor:   12.981


  62 in total

1.  Structural proteomics of an archaeon.

Authors:  D Christendat; A Yee; A Dharamsi; Y Kluger; A Savchenko; J R Cort; V Booth; C D Mackereth; V Saridakis; I Ekiel; G Kozlov; K L Maxwell; N Wu; L P McIntosh; K Gehring; M A Kennedy; A R Davidson; E F Pai; M Gerstein; A M Edwards; C H Arrowsmith
Journal:  Nat Struct Biol       Date:  2000-10

2.  Efforts to commercialize structural genomics may be limited

Authors: 
Journal:  Nat Biotechnol       Date:  2000-10       Impact factor: 54.908

3.  Mining the structural genomics pipeline: identification of protein properties that affect high-throughput experimental analysis.

Authors:  Chern-Sing Goh; Ning Lan; Shawn M Douglas; Baolin Wu; Nathaniel Echols; Andrew Smith; Duncan Milburn; Gaetano T Montelione; Hongyu Zhao; Mark Gerstein
Journal:  J Mol Biol       Date:  2004-02-06       Impact factor: 5.469

4.  Protein production and crystallization at the joint center for structural genomics.

Authors:  Scott A Lesley; Ian A Wilson
Journal:  J Struct Funct Genomics       Date:  2005

5.  Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy.

Authors:  Janet Newman; David Egan; Thomas S Walter; Ran Meged; Ian Berry; Marouane Ben Jelloul; Joel L Sussman; David I Stuart; Anastassis Perrakis
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2005-09-28

6.  Novel leverage of structural genomics.

Authors:  Jinfeng Liu; Gaetano T Montelione; Burkhard Rost
Journal:  Nat Biotechnol       Date:  2007-08       Impact factor: 54.908

Review 7.  100,000 protein structures for the biologist.

Authors:  A Sali
Journal:  Nat Struct Biol       Date:  1998-12

8.  Integrating structure, bioinformatics, and enzymology to discover function: BioH, a new carboxylesterase from Escherichia coli.

Authors:  Ruslan Sanishvili; Alexander F Yakunin; Roman A Laskowski; Tatiana Skarina; Elena Evdokimova; Amanda Doherty-Kirby; Gilles A Lajoie; Janet M Thornton; Cheryl H Arrowsmith; Alexei Savchenko; Andrzej Joachimiak; Aled M Edwards
Journal:  J Biol Chem       Date:  2003-05-05       Impact factor: 5.157

9.  Automated MAD and MIR structure solution.

Authors:  T C Terwilliger; J Berendzen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-04

10.  Crystal structure of the YffB protein from Pseudomonas aeruginosa suggests a glutathione-dependent thiol reductase function.

Authors:  Alexey Teplyakov; Sadhana Pullalarevu; Galina Obmolova; Victoria Doseeva; Andrey Galkin; Osnat Herzberg; Miroslawa Dauter; Zbigniew Dauter; Gary L Gilliland
Journal:  BMC Struct Biol       Date:  2004-03-08
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  48 in total

1.  Discrete molecular dynamics distinguishes nativelike binding poses from decoys in difficult targets.

Authors:  Elizabeth A Proctor; Shuangye Yin; Alexander Tropsha; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2012-01-03       Impact factor: 4.033

2.  Use of structural phylogenetic networks for classification of the ferritin-like superfamily.

Authors:  Daniel Lundin; Anthony M Poole; Britt-Marie Sjöberg; Martin Högbom
Journal:  J Biol Chem       Date:  2012-04-25       Impact factor: 5.157

3.  Computational design of a protein crystal.

Authors:  Christopher J Lanci; Christopher M MacDermaid; Seung-gu Kang; Rudresh Acharya; Benjamin North; Xi Yang; X Jade Qiu; William F DeGrado; Jeffery G Saven
Journal:  Proc Natl Acad Sci U S A       Date:  2012-04-25       Impact factor: 11.205

4.  Abstractions, algorithms and data structures for structural bioinformatics in PyCogent.

Authors:  Marcin Cieślik; Zygmunt S Derewenda; Cameron Mura
Journal:  J Appl Crystallogr       Date:  2011-02-11       Impact factor: 3.304

5.  Biocrystallography: past, present, future.

Authors:  Richard Giegé; Claude Sauter
Journal:  HFSP J       Date:  2010-04-22

6.  Structure- and sequence-based function prediction for non-homologous proteins.

Authors:  Lee Sael; Meghana Chitale; Daisuke Kihara
Journal:  J Struct Funct Genomics       Date:  2012-01-22

7.  Development of a full-length human protein production pipeline.

Authors:  Justin Saul; Brianne Petritis; Sujay Sau; Femina Rauf; Michael Gaskin; Benjamin Ober-Reynolds; Irina Mineyev; Mitch Magee; John Chaput; Ji Qiu; Joshua LaBaer
Journal:  Protein Sci       Date:  2014-06-02       Impact factor: 6.725

Review 8.  Strategies for protein synthetic biology.

Authors:  Raik Grünberg; Luis Serrano
Journal:  Nucleic Acids Res       Date:  2010-04-12       Impact factor: 16.971

9.  Mathematical model for empirically optimizing large scale production of soluble protein domains.

Authors:  Eisuke Chikayama; Atsushi Kurotani; Takanori Tanaka; Takashi Yabuki; Satoshi Miyazaki; Shigeyuki Yokoyama; Yutaka Kuroda
Journal:  BMC Bioinformatics       Date:  2010-03-01       Impact factor: 3.169

10.  SGC--structural biology and human health: a new approach to publishing structural biology results.

Authors:  Wen Hwa Lee; Julián Atienza-Herrero; Ruben Abagyan; Brian D Marsden
Journal:  PLoS One       Date:  2009-10-20       Impact factor: 3.240

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