R3XW38 last accessed: 2022-11-04

Nucleic Acid Database (NDB)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

ndb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

Other names: NDB, Nucleic Acid Database, A Portal for Three-dimensional Structural Information about Nucleic Acids, Nucleic Acid Database (NDB), ndb

The Nucleic Acids Database contains information about experimentally-determined nucleic acids and complex assemblies. NDB can be used to perform searches based on annotations relating to sequence, structure and function, and to download, analyze, and learn about nucleic acids.

Webpage:

http://ndbserver.rutgers.edu/

Licence:

Name: Copyrights
URL: https://it.rutgers.edu/policies/

Publications:

Publications
More detailed information about this field from each metasource.

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
PMID: 1384741
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

The Nucleic Acid Database: new features and capabilities
PMID: 24185695
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

The Nucleic Acid Database: Present and Future
PMID: 27805162
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

http://dx.doi.org/10.1093/nar/gkt980
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids PubMed citations: 296.

296 articles citing: The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

RNABPDB: Molecular Modeling of RNA Structure-From Base Pair Analysis in Crystals to Structure Prediction. PMID:35705797
Developing Community Resources for Nucleic Acid Structures. PMID:35455031
Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. PMID:35134335
Accurate prediction of B-form/A-form DNA conformation propensity from primary sequence: A machine learning and free energy handshake. PMID:34553171
RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources. PMID:34496744
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. PMID:34473508
Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity. PMID:34038115
Modeling and Predicting RNA Three-Dimensional Structures. PMID:33835435
An RNA-centric historical narrative around the Protein Data Bank. PMID:33744291
A comparative study of protein-ssDNA interactions. PMID:33655206
Advances in RNA 3D Structure Modeling Using Experimental Data. PMID:33193680
Systematics for types and effects of RNA variations. PMID:32951567
Landscape of DNA binding signatures of myocyte enhancer factor-2B reveals a unique interplay of base and shape readout. PMID:32738045
Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. PMID:32725210
The data universe of structural biology. PMID:32695409
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. PMID:32448174
How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. PMID:32243832
Multiple protein-DNA interfaces unravelled by evolutionary information, physico-chemical and geometrical properties. PMID:32012150
Study of the binding mechanism of aptamer to palytoxin by docking and molecular simulation. PMID:31664144
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures. PMID:31114927
Systematics for types and effects of DNA variations. PMID:30591019
Phylogenetic and mutational analyses of human LEUTX, a homeobox gene implicated in embryogenesis. PMID:30479355
Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins. PMID:29843482
bpRNA: large-scale automated annotation and analysis of RNA secondary structure. PMID:29746666
Topological Constraints and Their Conformational Entropic Penalties on RNA Folds. PMID:29742400
Probing the role of intercalating protein sidechains for kink formation in DNA. PMID:29432448
Biologically important conformational features of DNA as interpreted by quantum mechanics and molecular mechanics computations of its simple fragments. PMID:29392428
Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding. PMID:29165643
Intrinsic structural variability in GNRA-like tetraloops: insight from molecular dynamics simulation. PMID:28965269
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. PMID:28625696
SPA-LN: a scoring function of ligand-nucleic acid interactions via optimizing both specificity and affinity. PMID:28431169
Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. PMID:28158755
Statistics of topological RNA structures. PMID:27853818
In silico structural analysis of quorum sensing genes inVibriofischeri. PMID:27844003
Conventional and Eccentric Uses of Crystallographic Databases in Practical Materials Identification Problems. PMID:27805165
The Nucleic Acid Database: Present and Future. PMID:27805162
The archiving and dissemination of biological structure data. PMID:27450113
DETECTING CONFORMATIONAL DIFFERENCES BETWEEN RNA 3D STRUCTURES. PMID:27330250
Diffraction Techniques in Structural Biology. PMID:27248784
Structure elucidation of the Pribnow box consensus promoter sequence by racemic DNA crystallography. PMID:27137886
A Water-Soluble Tetraazaperopyrene Dye as Strong G-Quadruplex DNA Binder. PMID:26997208
Can Nucleobase Pairs Offer a Possibility of a Direct 3D Self-assembly? PMID:26956603
Biochemical Methods To Investigate lncRNA and the Influence of lncRNA:Protein Complexes on Chromatin. PMID:26859437
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. PMID:26827237
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. PMID:26478223
New in silico approach to assessing RNA secondary structures with non-canonical base pairs. PMID:26329823
3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures. PMID:25712091
Differential Impact of the Monovalent Ions Li⁺, Na⁺, K⁺, and Rb⁺ on DNA Conformational Properties. PMID:25580188
Arginine-phosphate salt bridges between histones and DNA: intermolecular actuators that control nucleosome architecture. PMID:25362343
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). PMID:25219455
Phosphates in the Z-DNA dodecamer are flexible, but their P-SAD signal is sufficient for structure solution. PMID:25004957
Analysis of stacking overlap in nucleic acid structures: algorithm and application. PMID:24990628
Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries. PMID:24914984
A statistical thermodynamic model for investigating the stability of DNA sequences from oligonucleotides to genomes. PMID:24896126
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field. PMID:24874104
Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms. PMID:24791158
All-atom polarizable force field for DNA based on the classical Drude oscillator model. PMID:24752978
Prediction of RNA binding residues: an extensive analysis based on structure and function to select the best predictor. PMID:24658593
Molecular modeling of nucleic acid structure. PMID:24510799
5-Methylation of cytosine in CG:CG base-pair steps: a physicochemical mechanism for the epigenetic control of DNA nanomechanics. PMID:24313757
The Nucleic Acid Database: new features and capabilities. PMID:24185695
Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions. PMID:23940752
An innate twist between Crick's wobble and Watson-Crick base pairs. PMID:23861536
Automatic workflow for the classification of local DNA conformations. PMID:23800225
Novel approach for selecting the best predictor for identifying the binding sites in DNA binding proteins. PMID:23788679
The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective. PMID:23695796
Three-dimensional RNA structure of the major HIV-1 packaging signal region. PMID:23685210
Strong bending of the DNA double helix. PMID:23677618
Analyzing and building nucleic acid structures with 3DNA. PMID:23644419
Nucleic acid helix structure determination from NMR proton chemical shifts. PMID:23564038
NPIDB: Nucleic acid-Protein Interaction DataBase. PMID:23193292
Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex. PMID:23192018
Coarse-grained prediction of RNA loop structures. PMID:23144887
Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore. PMID:23043363
Structure of d(CCGGGACCGG)4 as a four-way junction at 1.6 Å resolution: new insights into solvent interactions. PMID:23027741
Exploring polymorphisms in B-DNA helical conformations. PMID:23012264
The ABCs of molecular dynamics simulations on B-DNA, circa 2012. PMID:22750978
iHAT: interactive hierarchical aggregation table for genetic association data. PMID:22607364
Evolving stochastic context--free grammars for RNA secondary structure prediction. PMID:22559985
Automated 3D structure composition for large RNAs. PMID:22539264
Towards automated crystallographic structure refinement with phenix.refine. PMID:22505256
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium. PMID:22368531
Metal-adeninate vertices for the construction of an exceptionally porous metal-organic framework. PMID:22215079
Predicting RNA-protein interactions using only sequence information. PMID:22192482
Structure of d(CGGGTACCCG)4 as a four-way Holliday junction. PMID:22139153
RNA CoSSMos: Characterization of Secondary Structure Motifs--a searchable database of secondary structure motifs in RNA three-dimensional structures. PMID:22127861
Crystallography Open Database (COD): an open-access collection of crystal structures and platform for world-wide collaboration. PMID:22070882
Evaluation of DNA Force Fields in Implicit Solvation. PMID:22043178
A new way to see RNA. PMID:21729350
Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data. PMID:21716650
A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. PMID:21685058
RAG: an update to the RNA-As-Graphs resource. PMID:21627789
WebFR3D--a server for finding, aligning and analyzing recurrent RNA 3D motifs. PMID:21515634
High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A. PMID:21459852
Identifying and searching for conserved RNA localisation signals. PMID:21431757
Nucleic-acid structural deformability deduced from anisotropic displacement parameters. PMID:21280021
Properties of the Nucleic-acid Bases in Free and Watson-Crick Hydrogen-bonded States: Computational Insights into the Sequence-dependent Features of Double-helical DNA. PMID:21218180
Geometric properties of nucleic acids with potential for autobuilding. PMID:21173468
Nonparametric clustering for studying RNA conformations. PMID:21173460
Predicting RNA-binding residues from evolutionary information and sequence conservation. PMID:21143803
Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites. PMID:21124945
PRIDB: a Protein-RNA interface database. PMID:21071426
Joint X-ray and neutron refinement with phenix.refine. PMID:21041930
Computational approaches for RNA energy parameter estimation. PMID:20940338
Undulations enhance the effect of helical structure on DNA interactions. PMID:20718454
Environment influences on the aromatic character of nucleobases and amino acids. PMID:20668897
Long-range effects of histone point mutations on DNA remodeling revealed from computational analyses of SIN-mutant nucleosome structures. PMID:20647418
Diffraction techniques in structural biology. PMID:20517991
Structural and energetic consequences of oxidation of d(ApGpGpGpTpT) telomere repeat unit in complex with TRF1 protein. PMID:20464436
Non-additive interactions of nucleobases in model dinucleotide steps occurring in B-DNA crystals. PMID:20449619
Crystallization and preliminary X-ray diffraction analysis of a self-complementary DNA heptacosamer with a 20-base-pair duplex flanked by seven-nucleotide overhangs at the 3'-terminus. PMID:20445254
Urea facilitates the translocation of single-stranded DNA and RNA through the alpha-hemolysin nanopore. PMID:20441749
Semiautomated model building for RNA crystallography using a directed rotameric approach. PMID:20404211
Crystallization and preliminary X-ray study of the D-altritol oligonucleotide GTGTACAC. PMID:20383022
The many twists and turns of DNA: template, telomere, tool, and target. PMID:20381338
DNA architecture, deformability, and nucleosome positioning. PMID:20232929
The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex. PMID:20223772
Visualization of macromolecular structures. PMID:20195256
Visualization of multiple alignments, phylogenies and gene family evolution. PMID:20195253
Anomalous DNA binding by E2 regulatory protein driven by spacer sequence TATA. PMID:20185566
Helical chirality: a link between local interactions and global topology in DNA. PMID:20174470
Boosting the prediction and understanding of DNA-binding domains from sequence. PMID:20156993
Crystallographic studies of chemically modified nucleic acids: a backward glance. PMID:20087997
MolProbity: all-atom structure validation for macromolecular crystallography. PMID:20057044
DNA-binding residues and binding mode prediction with binding-mechanism concerned models. PMID:19958487
Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling. PMID:19923230
3DNALandscapes: a database for exploring the conformational features of DNA. PMID:19906722
Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. PMID:19861423
Molecular models for intrastrand DNA G-quadruplexes. PMID:19811654
Revisiting the planarity of nucleic acid bases: Pyramidilization at glycosidic nitrogen in purine bases is modulated by orientation of glycosidic torsion. PMID:19786496
3D-footprint: a database for the structural analysis of protein-DNA complexes. PMID:19767616
Influence of local sequence context on damaged base conformation in human DNA polymerase iota: molecular dynamics studies of nucleotide incorporation opposite a benzo[a]pyrene-derived adenine lesion. PMID:19767609
A generalized conformational energy function of DNA derived from molecular dynamics simulations. PMID:19729512
Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA. PMID:19708270
On the origin of life in the zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. PMID:19703275
Sequence dependencies of DNA deformability and hydration in the minor groove. PMID:19686662
PDA: an automatic and comprehensive analysis program for protein-DNA complex structures. PMID:19594872
A probabilistic model of RNA conformational space. PMID:19543381
SARA: a server for function annotation of RNA structures. PMID:19483098
Web 3DNA--a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. PMID:19474339
Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. PMID:19395592
Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. PMID:19393049
DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. PMID:19289051
Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. PMID:19193004
New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures. PMID:19150407
Structural and energetic heterogeneities of canonical and oxidized central guanine triad of B-DNA telomeric fragments. PMID:19132417
The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d(CpG) and d(GpC) steps found in B-DNA, A-DNA and Z-DNA crystals. PMID:19039609
Informatic resources for identifying and annotating structural RNA motifs. PMID:18979204
Automated motif extraction and classification in RNA tertiary structures. PMID:18957493
Annotation of tertiary interactions in RNA structures reveals variations and correlations. PMID:18957492
RsiteDB: a database of protein binding pockets that interact with RNA nucleotide bases. PMID:18953028
BPS: a database of RNA base-pair structures. PMID:18845572
Structural segments and residue propensities in protein-RNA interfaces: comparison with protein-protein and protein-DNA complexes. PMID:18841236
Helical coherence of DNA in crystals and solution. PMID:18755709
RNA STRAND: the RNA secondary structure and statistical analysis database. PMID:18700982
Protein-DNA interactions: the story so far and a new method for prediction. PMID:18629075
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. PMID:18600227
LocalMove: computing on-lattice fits for biopolymers. PMID:18556754
SARSA: a web tool for structural alignment of RNA using a structural alphabet. PMID:18502774
DNA conformations and their sequence preferences. PMID:18477633
Prediction of interacting single-stranded RNA bases by protein-binding patterns. PMID:18452949
An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions. PMID:18445289
Molecular modeling of nucleic acid structure. PMID:18428873
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). PMID:18192612
Indirect readout in drug-DNA recognition: role of sequence-dependent DNA conformation. PMID:18039704
Computational study on mechanism of G-quartet oligonucleotide T40214 selectively targeting Stat3. PMID:18034310
The Proteomic Code: a molecular recognition code for proteins. PMID:17999762
Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. PMID:17947978
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign. PMID:17947325
Mechanism of DNA-binding loss upon single-point mutation in p53. PMID:17914225
Backbone-base inclination as a fundamental determinant of nucleic acid self- and cross-pairing. PMID:17905816
Construction of a genome-scale structural map at single-nucleotide resolution. PMID:17568010
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. PMID:17452350
RNA localization signals: deciphering the message with bioinformatics. PMID:17452113
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone. PMID:17401565
X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative. PMID:17145714
Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis. PMID:17124630
The complex of ethidium bromide with genomic DNA: structure analysis by polarized Raman spectroscopy. PMID:17098786
Impact of static and dynamic A-form heterogeneity on the determination of RNA global structural dynamics using NMR residual dipolar couplings. PMID:17077936
Structural analysis of the catalytic core of human telomerase RNA by FRET and molecular modeling. PMID:17073451
MultiSeq: unifying sequence and structure data for evolutionary analysis. PMID:16914055
Indications that "codon boundaries" are physico-chemically defined and that protein-folding information is contained in the redundant exon bases. PMID:16893453
oGNM: online computation of structural dynamics using the Gaussian Network Model. PMID:16845002
Mutagenic nucleotide incorporation and hindered translocation by a food carcinogen C8-dG adduct in Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): modeling and dynamics studies. PMID:16820532
Flexible 5-guanidino-4-nitroimidazole DNA lesions: structures and thermodynamics. PMID:16716075
The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs. PMID:16581850
Incorporation of a disaccharide nucleoside into the backbone of double-stranded DNA: crystallization and preliminary X-ray diffraction. PMID:16511205
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex. PMID:16492787
The RNA Ontology Consortium: an open invitation to the RNA community. PMID:16484377
A new anti conformation for N-(deoxyguanosin-8-yl)-2-acetylaminofluorene (AAF-dG) allows Watson-Crick pairing in the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4). PMID:16452300
The Kernel Energy Method: application to a tRNA. PMID:16432197
MeRNA: a database of metal ion binding sites in RNA structures. PMID:16381830
Binding-linked protonation of a DNA minor-groove agent. PMID:16299076
The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA. PMID:16214808
Syntheses of 4'-thioribonucleosides and thermodynamic stability and crystal structure of RNA oligomers with incorporated 4'-thiocytosine. PMID:16027443
Describing RNA structure by libraries of clustered nucleotide doublets. PMID:15993894
RNA structure: the long and the short of it. PMID:15963891
Promoter addresses: revelations from oligonucleotide profiling applied to the Escherichia coli genome. PMID:15927055
Variable role of ions in two drug intercalation complexes of DNA. PMID:15926069
How sequence defines structure: a crystallographic map of DNA structure and conformation. PMID:15870206
Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information. PMID:15831786
Cyclization of short DNA fragments and bending fluctuations of the double helix. PMID:15809441
Knowledge-based elastic potentials for docking drugs or proteins with nucleic acids. PMID:15501936
RAG: RNA-As-Graphs web resource. PMID:15238163
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. PMID:15215462
Definitions and analysis of DNA Holliday junction geometry. PMID:15173384
Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. PMID:15121895
Dynamics of the B-A transition of DNA double helices. PMID:15107493
SCOR: Structural Classification of RNA, version 2.0. PMID:14681389
Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins. PMID:14654694
Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening. PMID:14654688
RNA backbone is rotameric. PMID:14612579
Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. PMID:14576313
Global mapping of nucleic acid conformational space: dinucleoside monophosphate conformations and transition pathways among conformational classes. PMID:14500824
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. PMID:12930962
RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. PMID:12907716
Molecular modeling of the chromatosome particle. PMID:12853645
Tools for the automatic identification and classification of RNA base pairs. PMID:12824344
Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. PMID:12771219
The crystal structure of the complex between a disaccharide anthracycline and the DNA hexamer d(CGATCG) reveals two different binding sites involving two DNA duplexes. PMID:12595554
The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs. PMID:12595546
RNABase: an annotated database of RNA structures. PMID:12520063
NTDB: Thermodynamic Database for Nucleic Acids, Version 2.0. PMID:12520057
MolMovDB: analysis and visualization of conformational change and structural flexibility. PMID:12520056
KDBI: Kinetic Data of Bio-molecular Interactions database. PMID:12519995
Alpha/gamma transitions in the B-DNA backbone. PMID:12490708
Mediation of the A/B-DNA helix transition by G-tracts in the crystal structure of duplex CATGGGCCCATG. PMID:12235390
The inherent properties of DNA four-way junctions: comparing the crystal structures of holliday junctions. PMID:12126623
RNAML: a standard syntax for exchanging RNA information. PMID:12088144
Accurate representation of B-DNA double helical structure with implicit solvent and counterions. PMID:12080128
The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex. PMID:12051940
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study. PMID:11867468
Protein and drug interactions in the minor groove of DNA. PMID:11861910
SCOR: a Structural Classification of RNA database. PMID:11752346
The IMB Jena Image Library of Biological Macromolecules: 2002 update. PMID:11752308
Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. PMID:11721003
X-ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 A). PMID:11707581
Crystal structures of two forms of a 14-mer RNA/DNA chimer duplex with double UU bulges: a novel intramolecular U*(A x U) base triple. PMID:11680847
Standard atomic volumes in double-stranded DNA and packing in protein--DNA interfaces. PMID:11504874
Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. PMID:11433033
A crystallographic map of the transition from B-DNA to A-DNA. PMID:11390969
Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments. PMID:11222771
Protein-RNA interactions: a structural analysis. PMID:11160927
The PDB data uniformity project. PMID:11125095
An overview of the structures of protein-DNA complexes. PMID:11104519
Synthesis and crystal structure of an octamer RNA r(guguuuac)/r(guaggcac) with G.G/U.U tandem wobble base pairs: comparison with other tandem G.U pairs. PMID:11058138
A novel form of intercalation involving four DNA duplexes in an acridine-4-carboxamide complex of d(CGTACG)(2). PMID:11058124
Crystal structure of a DNA.RNA hybrid duplex with a polypurine RNA r(gaagaagag) and a complementary polypyrimidine DNA d(CTCTTCTTC). PMID:10773088
Intermolecular interactions and water structure in a condensed phase B-DNA crystal. PMID:10666471
Structures of m-iodo Hoechst-DNA complexes in crystals with reduced solvent content: implications for minor groove binder drug design. PMID:10666470
Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment. PMID:10653780
The IMB Jena Image Library of biological macromolecules. PMID:10592237
The Protein Data Bank. PMID:10592235
A structural snapshot of base-pair opening in DNA. PMID:10518532
Sodium and chlorine ions as part of the DNA solvation shell. PMID:10512802
Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA. PMID:10354445
Molecular dynamics simulations of solvated yeast tRNA(Asp). PMID:9876122
Hydration of the phosphate group in double-helical DNA. PMID:9788937
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. PMID:9736707
Recommendations for the presentation of NMR structures of proteins and nucleic acids. IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. PMID:9729785
A database of macromolecular motions. PMID:9722650
Crystal structures of B-DNA with incorporated 2'-deoxy-2'-fluoro-arabino-furanosyl thymines: implications of conformational preorganization for duplex stability. PMID:9580702
Quantitative parameters for amino acid-base interaction: implications for prediction of protein-DNA binding sites. PMID:9580679
Hydration and recognition of methylated CpG steps in DNA. PMID:9564052
Non-complementary DNA helical structure induced by positive torsional stress. PMID:9490798
A terbenzimidazole that preferentially binds and conformationally alters structurally distinct DNA duplex domains: a potential mechanism for topoisomerase I poisoning. PMID:9391066
A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. PMID:9370428
Crystal structure of d(GCGCGCG) with 5'-overhang G residues. PMID:9284322
Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein. PMID:9251783
Influence of sequence on the conformation of the B-DNA helix. PMID:9199797
Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study. PMID:9199773
N-acyl-(alpha, gamma diaminobutyric acid)n hydrazide as an efficient gene transfer vector in mammalian cells in culture. PMID:9165533
Structure of a bis-amidinium derivative of hoechst 33258 complexed to dodecanucleotide d(CGCGAATTCGCG)2: the role of hydrogen bonding in minor groove drug-DNA recognition. PMID:9162901
The bi-loop, a new general four-stranded DNA motif. PMID:9159103
Application of a genetic algorithm in the conformational analysis of methylene-acetal-linked thymine dimers in DNA: comparison with distance geometry calculations. PMID:9081542
SCOP: a structural classification of proteins database. PMID:9016544
A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing. PMID:8917508
Inter-strand C-H...O hydrogen bonds stabilizing four-stranded intercalated molecules: stereoelectronic effects of O4' in cytosine-rich DNA. PMID:8901542
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II. PMID:8873996
Crystal structure of the self-complementary 5'-purine start decamer d(GCGCGCGCGC) in the Z-DNA conformation. I. PMID:8873995
H-bond stability in the tRNA(Asp) anticodon hairpin: 3 ns of multiple molecular dynamics simulations. PMID:8842234
Hydrogen bond geometry in DNA-minor groove binding drug complexes. PMID:8811103
Hydration of the DNA bases is local. PMID:8599672
NMR studies of DNA duplexes singly cross-linked by different synthetic linkers. PMID:8532525
A systematic method for studying the spatial distribution of water molecules around nucleic acid bases. PMID:8312469
Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes. PMID:8075315
Shape information from a critical point analysis of calculated electron density maps: application to DNA-drug systems. PMID:7964926
Stereoelectronic effects of deoxyribose O4' on DNA conformation. PMID:7816812
A trigonal form of the idarubicin:d(CGATCG) complex; crystal and molecular structure at 2.0 A resolution. PMID:7784175
The influence of salt on the structure and energetics of supercoiled DNA. PMID:7696459
Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. PMID:7647248
An A-DNA triplet code: thermodynamic rules for predicting A- and B-DNA. PMID:7604014
Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes. PMID:7542034
Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques. PMID:7521223
Low temperature structures of dCpG-proflavine. Conformational and hydration effects. PMID:1489914
The Nucleic Acid Database: new features and capabilities PubMed citations: 69.

69 articles citing: The Nucleic Acid Database: new features and capabilities

Novel Design of RNA Aptamers as Cancer Inhibitors and Diagnosis Targeting the Tyrosine Kinase Domain of the NT-3 Growth Factor Receptor Using a Computational Sequence-Based Approach. PMID:35889390
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
fingeRNAt-A novel tool for high-throughput analysis of nucleic acid-ligand interactions. PMID:35653385
Developing Community Resources for Nucleic Acid Structures. PMID:35455031
Thoughts on how to think (and talk) about RNA structure. PMID:35439059
Inherent conformational plasticity in dsRBDs enables interaction with topologically distinct RNAs. PMID:35134335
Structure-based deep learning for binding site detection in nucleic acid macromolecules. PMID:34859211
Conformational variability in proteins bound to single-stranded DNA: A new benchmark for new docking perspectives. PMID:34617336
ProNAB: database for binding affinities of protein-nucleic acid complexes and their mutants. PMID:34606614
Accurate prediction of B-form/A-form DNA conformation propensity from primary sequence: A machine learning and free energy handshake. PMID:34553171
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. PMID:34473508
Structure-based design of antisense oligonucleotides that inhibit SARS-CoV-2 replication. PMID:34462746
SHAPER: A Web Server for Fast and Accurate SHAPE Reactivity Prediction. PMID:34395533
A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PMID:34343165
An RNA-centric historical narrative around the Protein Data Bank. PMID:33744291
A comparative study of protein-ssDNA interactions. PMID:33655206
Sieving RNA 3D Structures with SHAPE and Evaluating Mechanisms Driving Sequence-Dependent Reactivity Bias. PMID:33497570
Advances in RNA 3D Structure Modeling Using Experimental Data. PMID:33193680
Comprehensive Survey and Comparative Assessment of RNA-Binding Residue Predictions with Analysis by RNA Type. PMID:32961749
Frequency and hydrogen bonding of nucleobase homopairs in small molecule crystals. PMID:32725210
RintC: fast and accuracy-aware decomposition of distributions of RNA secondary structures with extended logsumexp. PMID:32448174
DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. PMID:32442277
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How RNA-Binding Proteins Interact with RNA: Molecules and Mechanisms. PMID:32243832
PreDBA: A heterogeneous ensemble approach for predicting protein-DNA binding affinity. PMID:31992738
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DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
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RNA-protein interactions in an unstructured context. PMID:29851074
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Topological Constraints and Their Conformational Entropic Penalties on RNA Folds. PMID:29742400
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Probing the role of intercalating protein sidechains for kink formation in DNA. PMID:29432448
Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs. PMID:29354101
Interactions of 2'-O-methyl oligoribonucleotides with the RNA models of the 30S subunit A-site. PMID:29351348
R3D-BLAST2: an improved search tool for similar RNA 3D substructures. PMID:29297283
Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo. PMID:28625696
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Using sequence signatures and kink-turn motifs in knowledge-based statistical potentials for RNA structure prediction. PMID:28158755
Nucleoid and cytoplasmic localization of small RNAs in Escherichia coli. PMID:28119418
Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology. PMID:28064006
Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools. PMID:28035947
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Statistics of topological RNA structures. PMID:27853818
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Diffraction Techniques in Structural Biology. PMID:27248784
URS DataBase: universe of RNA structures and their motifs. PMID:27242032
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Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. PMID:26751501
BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data. PMID:26612862
Predicting Large RNA-Like Topologies by a Knowledge-Based Clustering Approach. PMID:26478223
R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server. PMID:26048960
Rsite: a computational method to identify the functional sites of noncoding RNAs. PMID:25776805
Biological databases for human research. PMID:25712261
High-resolution crystal structure of Z-DNA in complex with Cr(3+) cations. PMID:25687556
Protein structure annotation resources. PMID:25502191
Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC). PMID:25219455
Enhancing UCSF Chimera through web services. PMID:24861624
The 2014 Nucleic Acids Research Database Issue and an updated NAR online Molecular Biology Database Collection. PMID:24316579
The Nucleic Acid Database: Present and Future PubMed citations: 0.

0 articles citing: The Nucleic Acid Database: Present and Future
http://dx.doi.org/10.1093/nar/gkt980

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deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

nucleic acid sequence
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

ribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: NDB; Nucleic Acids Database; DOI: https://doi.org/10.25504/FAIRsharing.bh0k78; Last edited: April 26, 2021, 2:59 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

nucleic acid structure
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

dna
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

rna
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

nucleid acids
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

nucleotides
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

nuclopeptides
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

nucloproteins
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: Nucleic Acid Database; editing status 2022-08-19; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3XW38 last accessed: 2022-11-04

nucleic acids
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

nucleic acid structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

sequence composition, complexity and repeats
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

nucleic acid sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:55.339878

dna nucleic acid sequence rna structure nucleic acid structure dna rna bioinformatics nucleid acids nucleotides nuclopeptides nucloproteins proteins nucleic acids nucleic acid structure analysis structure prediction sequence composition, complexity and repeats nucleic acid sites, features and motifs

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MINAS - A Database of Metal Ions in Nucleic AcidS

IUPAC-IUB Commission on Biochemical Nomenclature - Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents

Nucleic Acid Phylogenetic Profile

Big Data Nucleic Acid Simulations Database

ProNAB

NNDB

LINCS Extended Metadata Standard: Nucleic Acid Reagents

NPIDB (Nucleic acids Ã¢â‚¬â€œ Protein Interaction DataBase)

Biological Magnetic Resonance Databank

RNA Characterization of Secondary Structure Motifs

Ligand Expo

SMMRNA

InterRNA

Jenalib: Jena Library of Biological Macromolecules

IBIS

ONQUADRO

RNA Bricks

MetalPDB

RCSB Protein Data Bank

Voronoia4RNA