Literature DB >> 18542858

Data deposition and annotation at the worldwide protein data bank.

Shuchismita Dutta1, Kyle Burkhardt, Ganesh J Swaminathan, Takashi Kosada, Kim Henrick, Haruki Nakamura, Helen M Berman.   

Abstract

The Protein Data Bank (PDB) is the repository for the three-dimensional structures of biological macromolecules, determined by experimental methods. The data in the archive are free and easily available via the Internet from any of the worldwide centers managing this global archive. These data are used by scientists, researchers, bioinformatics specialists, educators, students, and lay audiences to understand biological phenomena at a molecular level. Analysis of these structural data also inspires and facilitates new discoveries in science. This chapter describes the tools and methods currently used for deposition, processing, and release of data in the PDB. References to future enhancements are also included.

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Year:  2008        PMID: 18542858     DOI: 10.1007/978-1-60327-058-8_5

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  9 in total

1.  A Multimodal Data Analysis Approach for Targeted Drug Discovery Involving Topological Data Analysis (TDA).

Authors:  Muthuraman Alagappan; Dadi Jiang; Nicholas Denko; Albert C Koong
Journal:  Adv Exp Med Biol       Date:  2016       Impact factor: 2.622

2.  Impact of Double Covalent Binding of BV in NIR FPs on Their Spectral and Physicochemical Properties.

Authors:  Olga V Stepanenko; Irina M Kuznetsova; Konstantin K Turoverov; Olesya V Stepanenko
Journal:  Int J Mol Sci       Date:  2022-07-01       Impact factor: 6.208

3.  Dual targeting of a tRNAAsp requires two different aspartyl-tRNA synthetases in Trypanosoma brucei.

Authors:  Fabien Charrière; Patrick O'Donoghue; Sunna Helgadóttir; Laurence Maréchal-Drouard; Marina Cristodero; Elke K Horn; Dieter Söll; André Schneider
Journal:  J Biol Chem       Date:  2009-04-22       Impact factor: 5.157

4.  X-ray structure and kinetic properties of ornithine transcarbamoylase from the human parasite Giardia lamblia.

Authors:  Andrey Galkin; Liudmila Kulakova; Rui Wu; Maozhen Gong; Debra Dunaway-Mariano; Osnat Herzberg
Journal:  Proteins       Date:  2009-09

5.  ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.

Authors:  Pier L Martelli; Mattia D'Antonio; Paola Bonizzoni; Tiziana Castrignanò; Anna M D'Erchia; Paolo D'Onorio De Meo; Piero Fariselli; Michele Finelli; Flavio Licciulli; Marina Mangiulli; Flavio Mignone; Giulio Pavesi; Ernesto Picardi; Raffaella Rizzi; Ivan Rossi; Alessio Valletti; Andrea Zauli; Federico Zambelli; Rita Casadio; Graziano Pesole
Journal:  Nucleic Acids Res       Date:  2010-11-04       Impact factor: 16.971

6.  Structure based annotation of Helicobacter pylori strain 26695 proteome.

Authors:  Swati Singh; Praveen Kumar Guttula; Lalitha Guruprasad
Journal:  PLoS One       Date:  2014-12-30       Impact factor: 3.240

7.  RAPID: Resource of Asian Primary Immunodeficiency Diseases.

Authors:  Shivakumar Keerthikumar; Rajesh Raju; Kumaran Kandasamy; Atsushi Hijikata; Subhashri Ramabadran; Lavanya Balakrishnan; Mukhtar Ahmed; Sandhya Rani; Lakshmi Dhevi N Selvan; Devi S Somanathan; Somak Ray; Mitali Bhattacharjee; Sashikanth Gollapudi; Y L Ramachandra; Sahely Bhadra; Chiranjib Bhattacharyya; Kohsuke Imai; Shigeaki Nonoyama; Hirokazu Kanegane; Toshio Miyawaki; Akhilesh Pandey; Osamu Ohara; Sujatha Mohan
Journal:  Nucleic Acids Res       Date:  2008-10-08       Impact factor: 16.971

8.  HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.

Authors:  Panagiotis L Kastritis; João P G L M Rodrigues; Alexandre M J J Bonvin
Journal:  J Chem Inf Model       Date:  2014-02-27       Impact factor: 4.956

9.  Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining.

Authors:  Zbigniew Dauter; Alexander Wlodawer; Wladek Minor; Mariusz Jaskolski; Bernhard Rupp
Journal:  IUCrJ       Date:  2014-04-14       Impact factor: 4.769

  9 in total

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