Literature DB >> 21225378

Protein structure databases.

Roman A Laskowski1.   

Abstract

Web-based protein structure databases come in a wide variety of types and levels of information content. Those having the most general interest are the various atlases that describe each experimentally determined protein structure and provide useful links, analyses and schematic diagrams relating to its 3D structure and biological function. Also of great interest are the databases that classify 3D structures by their folds as these can reveal evolutionary relationships which may be hard to detect from sequence comparison alone. Related to these are the numerous servers that compare folds-particularly useful for newly solved structures, and especially those of unknown function. Beyond these there are a vast number of databases for the most specialized user, dealing with specific families, diseases, structural features and so on.

Mesh:

Year:  2011        PMID: 21225378     DOI: 10.1007/s12033-010-9372-4

Source DB:  PubMed          Journal:  Mol Biotechnol        ISSN: 1073-6085            Impact factor:   2.695


  67 in total

1.  The Protein Data Bank.

Authors:  H M Berman; J Westbrook; Z Feng; G Gilliland; T N Bhat; H Weissig; I N Shindyalov; P E Bourne
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

2.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

3.  E-MSD: an integrated data resource for bioinformatics.

Authors:  A Golovin; T J Oldfield; J G Tate; S Velankar; G J Barton; H Boutselakis; D Dimitropoulos; J Fillon; A Hussain; J M C Ionides; M John; P A Keller; E Krissinel; P McNeil; A Naim; R Newman; A Pajon; J Pineda; A Rachedi; J Copeland; A Sitnov; S Sobhany; A Suarez-Uruena; G J Swaminathan; M Tagari; S Tromm; W Vranken; K Henrick
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  PROSITE: a documented database using patterns and profiles as motif descriptors.

Authors:  Christian J A Sigrist; Lorenzo Cerutti; Nicolas Hulo; Alexandre Gattiker; Laurent Falquet; Marco Pagni; Amos Bairoch; Philipp Bucher
Journal:  Brief Bioinform       Date:  2002-09       Impact factor: 11.622

5.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

6.  The ConSurf-HSSP database: the mapping of evolutionary conservation among homologs onto PDB structures.

Authors:  Fabian Glaser; Yossi Rosenberg; Amit Kessel; Tal Pupko; Nir Ben-Tal
Journal:  Proteins       Date:  2005-02-15

7.  A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules.

Authors:  Rolf Hühne; Frank-Thomas Koch; Jürgen Sühnel
Journal:  Brief Funct Genomic Proteomic       Date:  2007-10-23

8.  ASD: a comprehensive database of allosteric proteins and modulators.

Authors:  Zhimin Huang; Liang Zhu; Yan Cao; Geng Wu; Xinyi Liu; Yingyi Chen; Qi Wang; Ting Shi; Yaxue Zhao; Yuefei Wang; Weihua Li; Yixue Li; Haifeng Chen; Guoqiang Chen; Jian Zhang
Journal:  Nucleic Acids Res       Date:  2010-11-04       Impact factor: 16.971

9.  The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.

Authors:  Frances Pearl; Annabel Todd; Ian Sillitoe; Mark Dibley; Oliver Redfern; Tony Lewis; Christopher Bennett; Russell Marsden; Alistair Grant; David Lee; Adrian Akpor; Michael Maibaum; Andrew Harrison; Timothy Dallman; Gabrielle Reeves; Ilhem Diboun; Sarah Addou; Stefano Lise; Caroline Johnston; Antonio Sillero; Janet Thornton; Christine Orengo
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

10.  E-MSD: an integrated data resource for bioinformatics.

Authors:  S Velankar; P McNeil; V Mittard-Runte; A Suarez; D Barrell; R Apweiler; K Henrick
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

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