Literature DB >> 12037326

The Nucleic Acid Database.

Helen M Berman1, John Westbrook, Zukang Feng, Lisa Iype, Bohdan Schneider, Christine Zardecki.   

Abstract

The Nucleic Acid Database was established in 1991 as a resource to assemble and distribute structural information about nucleic acids. Over the years, the NDB has developed generalized software for processing, archiving, querying and distributing structural data for nucleic acid-containing structures. The architecture and capabilities of the Nucleic Acid Database, as well as some of the research enabled by this resource, are presented in this article.

Mesh:

Year:  2002        PMID: 12037326     DOI: 10.1107/s0907444902003487

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  23 in total

1.  Semantic integration of data on transcriptional regulation.

Authors:  Michael Baitaluk; Julia Ponomarenko
Journal:  Bioinformatics       Date:  2010-04-28       Impact factor: 6.937

2.  RNA folding: A clear path to RNA catalysis.

Authors:  Amanda Solem; Alain Laederach
Journal:  Nat Chem Biol       Date:  2015-12       Impact factor: 15.040

3.  Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences.

Authors:  Surjit B Dixit; David Q Andrews; D L Beveridge
Journal:  Biophys J       Date:  2005-02-24       Impact factor: 4.033

4.  Predicting helical coaxial stacking in RNA multibranch loops.

Authors:  Rahul Tyagi; David H Mathews
Journal:  RNA       Date:  2007-05-16       Impact factor: 4.942

5.  Analysis and classification of RNA tertiary structures.

Authors:  Mira Abraham; Oranit Dror; Ruth Nussinov; Haim J Wolfson
Journal:  RNA       Date:  2008-09-29       Impact factor: 4.942

6.  Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand.

Authors:  James P Hall; Kyra O'Sullivan; Abeer Naseer; Jayden A Smith; John M Kelly; Christine J Cardin
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-03       Impact factor: 11.205

7.  Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps.

Authors:  Surjit B Dixit; David L Beveridge; David A Case; Thomas E Cheatham; Emmanuel Giudice; Filip Lankas; Richard Lavery; John H Maddocks; Roman Osman; Heinz Sklenar; Kelly M Thayer; Péter Varnai
Journal:  Biophys J       Date:  2005-09-16       Impact factor: 4.033

8.  Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

Authors:  Scott Quarrier; Joshua S Martin; Lauren Davis-Neulander; Arthur Beauregard; Alain Laederach
Journal:  RNA       Date:  2010-04-22       Impact factor: 4.942

9.  JAIL: a structure-based interface library for macromolecules.

Authors:  Stefan Günther; Joachim von Eichborn; Patrick May; Robert Preissner
Journal:  Nucleic Acids Res       Date:  2008-10-02       Impact factor: 16.971

10.  FASTR3D: a fast and accurate search tool for similar RNA 3D structures.

Authors:  Chin-En Lai; Ming-Yuan Tsai; Yun-Chen Liu; Chih-Wei Wang; Kun-Tze Chen; Chin Lung Lu
Journal:  Nucleic Acids Res       Date:  2009-05-12       Impact factor: 16.971

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