Literature DB >> 22527514

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.

Lida K Gifford1, Lester G Carter, Margaret J Gabanyi, Helen M Berman, Paul D Adams.   

Abstract

The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.

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Year:  2012        PMID: 22527514      PMCID: PMC3588887          DOI: 10.1007/s10969-012-9133-7

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


  33 in total

1.  SPINE: an integrated tracking database and data mining approach for identifying feasible targets in high-throughput structural proteomics.

Authors:  P Bertone; Y Kluger; N Lan; D Zheng; D Christendat; A Yee; A M Edwards; C H Arrowsmith; G T Montelione; M Gerstein
Journal:  Nucleic Acids Res       Date:  2001-07-01       Impact factor: 16.971

2.  SPINS: standardized protein NMR storage. A data dictionary and object-oriented relational database for archiving protein NMR spectra.

Authors:  Michael C Baran; Hunter N B Moseley; Gurmukh Sahota; Gaetano T Montelione
Journal:  J Biomol NMR       Date:  2002-10       Impact factor: 2.835

3.  2dx--user-friendly image processing for 2D crystals.

Authors:  Bryant Gipson; Xiangyan Zeng; Zi Yan Zhang; Henning Stahlberg
Journal:  J Struct Biol       Date:  2006-09-01       Impact factor: 2.867

4.  2dx_merge: data management and merging for 2D crystal images.

Authors:  Bryant Gipson; Xiangyan Zeng; Henning Stahlberg
Journal:  J Struct Biol       Date:  2007-09-25       Impact factor: 2.867

5.  Toward rational protein crystallization: A Web server for the design of crystallizable protein variants.

Authors:  Lukasz Goldschmidt; David R Cooper; Zygmunt S Derewenda; David Eisenberg
Journal:  Protein Sci       Date:  2007-08       Impact factor: 6.725

6.  Targeting the human cancer pathway protein interaction network by structural genomics.

Authors:  Yuanpeng Janet Huang; Dehua Hang; Long Jason Lu; Liang Tong; Mark B Gerstein; Gaetano T Montelione
Journal:  Mol Cell Proteomics       Date:  2008-05-18       Impact factor: 5.911

7.  TOPSAN: a dynamic web database for structural genomics.

Authors:  Kyle Ellrott; Christian M Zmasek; Dana Weekes; S Sri Krishna; Constantina Bakolitsa; Adam Godzik; John Wooley
Journal:  Nucleic Acids Res       Date:  2010-10-20       Impact factor: 16.971

8.  ModBase, a database of annotated comparative protein structure models, and associated resources.

Authors:  Ursula Pieper; Benjamin M Webb; David T Barkan; Dina Schneidman-Duhovny; Avner Schlessinger; Hannes Braberg; Zheng Yang; Elaine C Meng; Eric F Pettersen; Conrad C Huang; Ruchira S Datta; Parthasarathy Sampathkumar; Mallur S Madhusudhan; Kimmen Sjölander; Thomas E Ferrin; Stephen K Burley; Andrej Sali
Journal:  Nucleic Acids Res       Date:  2010-11-19       Impact factor: 16.971

9.  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

10.  Prolinks: a database of protein functional linkages derived from coevolution.

Authors:  Peter M Bowers; Matteo Pellegrini; Mike J Thompson; Joe Fierro; Todd O Yeates; David Eisenberg
Journal:  Genome Biol       Date:  2004-04-16       Impact factor: 13.583

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  15 in total

1.  Revealing the hidden functional diversity of an enzyme family.

Authors:  Karine Bastard; Adam Alexander Thil Smith; Carine Vergne-Vaxelaire; Alain Perret; Anne Zaparucha; Raquel De Melo-Minardi; Aline Mariage; Magali Boutard; Adrien Debard; Christophe Lechaplais; Christine Pelle; Virginie Pellouin; Nadia Perchat; Jean-Louis Petit; Annett Kreimeyer; Claudine Medigue; Jean Weissenbach; François Artiguenave; Véronique De Berardinis; David Vallenet; Marcel Salanoubat
Journal:  Nat Chem Biol       Date:  2013-11-17       Impact factor: 15.040

2.  Quantitative characterization of bovine serum albumin thin-films using terahertz spectroscopy and machine learning methods.

Authors:  Yiwen Sun; Pengju Du; Xingxing Lu; Pengfei Xie; Zhengfang Qian; Shuting Fan; Zexuan Zhu
Journal:  Biomed Opt Express       Date:  2018-06-06       Impact factor: 3.732

3.  Annotation of proteins of unknown function: initial enzyme results.

Authors:  Talia McKay; Kaitlin Hart; Alison Horn; Haeja Kessler; Greg Dodge; Keti Bardhi; Kostandina Bardhi; Jeffrey L Mills; Herbert J Bernstein; Paul A Craig
Journal:  J Struct Funct Genomics       Date:  2015-01-29

4.  Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative.

Authors:  Kamil Khafizov; Carlos Madrid-Aliste; Steven C Almo; Andras Fiser
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-24       Impact factor: 11.205

5.  BioMagResBank (BMRB) as a Resource for Structural Biology.

Authors:  Pedro R Romero; Naohiro Kobayashi; Jonathan R Wedell; Kumaran Baskaran; Takeshi Iwata; Masashi Yokochi; Dimitri Maziuk; Hongyang Yao; Toshimichi Fujiwara; Genji Kurusu; Eldon L Ulrich; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2020

Review 6.  Protein structure annotation resources.

Authors:  Margaret J Gabanyi; Helen M Berman
Journal:  Methods Mol Biol       Date:  2015

Review 7.  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 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.  An atypical orphan carbohydrate-NRPS genomic island encodes a novel lytic transglycosylase.

Authors:  Xun Guo; Jason M Crawford
Journal:  Chem Biol       Date:  2014-09-11

10.  Protein function annotation by local binding site surface similarity.

Authors:  Russell Spitzer; Ann E Cleves; Rocco Varela; Ajay N Jain
Journal:  Proteins       Date:  2013-11-22
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