3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (Q41979786)

14 October 2017

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (English)

1 reference

14 October 2017

1 reference

0 references

Xiang-Jun Lu

1

1 reference

PMCID

3065354

14 October 2017

Wilma K Olson

series ordinal

2

1 reference

14 October 2017

1 January 2008

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14 October 2017

1 reference

14 October 2017

3

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14 October 2017

1213-1227

1 reference

14 October 2017

7

1 reference

https://scigraph.springernature.com/pub.10.1038/nprot.2008.104

14 October 2017

0 references

cites work

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Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor

5 June 2018

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A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

5 June 2018

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Breaking pseudo-twofold symmetry in the poliovirus 3'-UTR Y-stem by restoring Watson-Crick base pairs

5 June 2018

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The ARTS web server for aligning RNA tertiary structures

5 June 2018

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Information-driven protein-DNA docking using HADDOCK: it is a matter of flexibility

5 June 2018

1 reference

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Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases

5 June 2018

1 reference

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PDBML: the representation of archival macromolecular structure data in XML.

5 June 2018

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Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The structure of DNA in the nucleosome core

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Sequence-dependent motions of DNA: a normal mode analysis at the base-pair level

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

A standard reference frame for the description of nucleic acid base-pair geometry.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The kink-turn: a new RNA secondary structure motif

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Geometric nomenclature and classification of RNA base pairs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

RNA tertiary interactions in the large ribosomal subunit: the A-minor motif

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The complete atomic structure of the large ribosomal subunit at 2.4 A resolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

A-form conformational motifs in ligand-bound DNA structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Alternative conformations of a nucleic acid four-way junction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

5 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

A detailed view of a ribosomal active site: the structure of the L11-RNA complex

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Protein-DNA interactions: A structural analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Overview of nucleic acid analysis programs

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Structure-based prediction of DNA target sites by regulatory proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Structural features of protein-nucleic acid recognition sites.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Resolving the discrepancies among nucleic acid conformational analyses

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

An analysis of the relationship between hydration and protein-DNA interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

A role for CH...O interactions in protein-DNA recognition.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DNA bending: the prevalence of kinkiness and the virtues of normality

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

NUCPLOT: a program to generate schematic diagrams of protein-nucleic acid interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Structure and conformation of helical nucleic acids: analysis program (SCHNAaP).

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DRAWNA: a program for drawing schematic views of nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

RASMOL: biomolecular graphics for all

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The pitch of chromatin DNA is reflected in its nucleotide sequence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DNA structural dynamics: longitudinal breathing as a possible mechanism for the B in equilibrium Z transition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Sequence dependence of the curvature of DNA: a test of the phasing hypothesis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

DNA bending at adenine . thymine tracts

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Estimation of wedge components in curved DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Defining the structure of irregular nucleic acids: conventions and principles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Anisotropic flexibility of DNA and the nucleosomal structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

SwS: a solvation web service for nucleic acids.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Statistical analysis of atomic contacts at RNA-protein interfaces

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3065354

Rules governing the orientation of the 2'-hydroxyl group in RNA

18 August 2018

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

DNA recognition by beta-sheets

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Structure and conformation of helical nucleic acids: rebuilding program (SCHNArP)

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Views of RNA on the World Wide Web

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Geometric Parameters in Nucleic Acids: Nitrogenous Bases

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

B-DNA twisting correlates with base-pair morphology.

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Sequence-directed curvature of DNA

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

Theoretical probes of DNA conformation examining the B leads to Z conformational transition

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

A Detailed View of a Ribosomal Active Site

31 March 2020

1 reference

https://api.crossref.org/works/10.1038%2FNPROT.2008.104

31 March 2020

Identifiers

DOI

10.1038/NPROT.2008.104

1 reference

release_4m476rojl5cqrd5e26kbaxuqkq

14 October 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/4m476rojl5cqrd5e26kbaxuqkq

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

3065354

1 reference

14 October 2017

1 reference

PMCID

3065354