NNDB

Names
More detailed information about this field from each metasource.

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

metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

nndb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

Other names: nndb

Nearest Neighbor parameters for predicting RNA folding

Webpage:

http://rna.urmc.rochester.edu/NNDB

Publications:

Publications
More detailed information about this field from each metasource.

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
PMID: 19880381
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

http://nar.oxfordjournals.org/content/38/suppl_1/D280
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure PubMed citations: 192.

192 articles citing: NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

SHAPE-guided RNA structure homology search and motif discovery. PMID:35361788
Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment. PMID:35269600
Landscape Zooming toward the Prediction of RNA Cotranscriptional Folding. PMID:35133833
RNA secondary structure prediction with convolutional neural networks. PMID:35109787
VfoldMCPX: predicting multistrand RNA complexes. PMID:35058350
Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides. PMID:34983822
Predicting the Structure of a Viroid : Structure, Structure Distribution, Consensus Structure, and Structure Drawing. PMID:34845705
Progress toward SHAPE Constrained Computational Prediction of Tertiary Interactions in RNA Structure. PMID:34842779
Beyond identity: Understanding the contribution of the 5' nucleotide of the antisense strand to RNAi activity. PMID:34492058
Vfold2D-MC: A Physics-Based Hybrid Model for Predicting RNA Secondary Structure Folding. PMID:34473508
Review of machine learning methods for RNA secondary structure prediction. PMID:34437528
Context-sensitivity of isosteric substitutions of non-Watson-Crick basepairs in recurrent RNA 3D motifs. PMID:34403481
The shaping of a molecular linguist: How a career studying DNA energetics revealed the language of molecular communication. PMID:34237886
Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene. PMID:34141448
Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. PMID:34127534
Towards an understanding of RNA structural modalities: a riboswitch case study. PMID:34113790
Diagrammatic approaches to RNA structures with trinucleotide repeats. PMID:33887227
Characteristic chemical probing patterns of loop motifs improve prediction accuracy of RNA secondary structures. PMID:33849076
Synonymous variants that disrupt messenger RNA structure are significantly constrained in the human population. PMID:33822938
Improving RNA Branching Predictions: Advances and Limitations. PMID:33805944
Whole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress. PMID:33758086
Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. PMID:33744957
RNA secondary structure prediction using deep learning with thermodynamic integration. PMID:33574226
RNAxplorer: Harnessing the Power of Guiding Potentials to Sample RNA Landscapes. PMID:33538792
ATTfold: RNA Secondary Structure Prediction With Pseudoknots Based on Attention Mechanism. PMID:33384721
RNA Secondary Structures with Limited Base Pair Span: Exact Backtracking and an Application. PMID:33374382
Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. PMID:33188057
PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region. PMID:33103602
On the Problem of Reconstructing a Mixture of RNA Structures. PMID:33029669
Genes with 5' terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 Nsp1 protein. PMID:32995776
microRNA strand selection: Unwinding the rules. PMID:32954644
Modeling Loop Composition and Ion Concentration Effects in RNA Hairpin Folding Stability. PMID:32949490
Beyond Plug and Pray: Context Sensitivity and in silico Design of Artificial Neomycin Riboswitches. PMID:32882151
A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions. PMID:32866223
Diverse enzymatic activities mediate antiviral immunity in prokaryotes. PMID:32855333
IPANEMAP: integrative probing analysis of nucleic acids empowered by multiple accessibility profiles. PMID:32735675
An in silico map of the SARS-CoV-2 RNA Structurome. PMID:32511381
A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures. PMID:32486951
Developments of Riboswitches and Toehold Switches for Molecular Detection-Biosensing and Molecular Diagnostics. PMID:32366036
How We Think about Targeting RNA with Small Molecules. PMID:32212706
Likelihood of Nonspecific Activity of Gapmer Antisense Oligonucleotides Is Associated with Relative Hybridization Free Energy. PMID:32125928
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. PMID:31978147
A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.). PMID:31976180
Understanding off-target effects through hybridization kinetics and thermodynamics. PMID:31823200
Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships. PMID:31717552
A robust model for quantitative prediction of the silencing efficacy of wild-type and A-to-I edited miRNAs. PMID:31601146
Apple chlorotic fruit spot viroid: a putative new pathogenic viroid on apple characterized by next-generation sequencing. PMID:31598842
Kinetic Mechanism of RNA Helix-Terminal Basepairing-A Kinetic Minima Network Analysis. PMID:31590890
Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination. PMID:31572840
Genetic robustness of let-7 miRNA sequence-structure pairs. PMID:31548338
ShaKer: RNA SHAPE prediction using graph kernel. PMID:31510707
On the emergence of structural complexity in RNA replicators. PMID:31467146
A Polymer Physics Framework for the Entropy of Arbitrary Pseudoknots. PMID:31353036
The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. PMID:31291322
RNA structural analysis of the MYC mRNA reveals conserved motifs that affect gene expression. PMID:31206539
A New Method of RNA Secondary Structure Prediction Based on Convolutional Neural Network and Dynamic Programming. PMID:31191603
Computational approaches for the discovery of splicing regulatory RNA structures. PMID:31048028
Fixed-parameter tractable sampling for RNA design with multiple target structures. PMID:31023239
Estimating uncertainty in predicted folding free energy changes of RNA secondary structures. PMID:30952689
RCPred: RNA complex prediction as a constrained maximum weight clique problem. PMID:30925864
Determining parameters for non-linear models of multi-loop free energy change. PMID:30923811
SSS-test: a novel test for detecting positive selection on RNA secondary structure. PMID:30898084
Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides. PMID:30846846
Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition. PMID:30753582
Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures. PMID:30702283
Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma. PMID:30581467
Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE. PMID:30559425
Chemically Accurate Relative Folding Stability of RNA Hairpins from Molecular Simulations. PMID:30375860
CRISPR-Cas9 off-targeting assessment with nucleic acid duplex energy parameters. PMID:30367669
Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions. PMID:30236782
Interactive implementations of thermodynamics-based RNA structure and RNA-RNA interaction prediction approaches for example-driven teaching. PMID:30161123
Challenges and approaches to predicting RNA with multiple functional structures. PMID:30143552
Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction. PMID:30104207
AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems. PMID:29986050
A Canonical Biophysical Model of the CsrA Global Regulator Suggests Flexible Regulator-Target Interactions. PMID:29967470
Topological Constraints and Their Conformational Entropic Penalties on RNA Folds. PMID:29742400
Improving RNA nearest neighbor parameters for helices by going beyond the two-state model. PMID:29718397
In the Beginning was a Mutualism - On the Origin of Translation. PMID:29713988
Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions. PMID:29694857
Quantitative Understanding of SHAPE Mechanism from RNA Structure and Dynamics Analysis. PMID:29659274
The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics. PMID:29576756
RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. PMID:29297679
Widespread temperature sensitivity and tRNA decay due to mutations in a yeast tRNA. PMID:29259051
Modeling RNA secondary structure folding ensembles using SHAPE mapping data. PMID:29177466
Swellix: a computational tool to explore RNA conformational space. PMID:29157200
An intermediate level of abstraction for computational systems chemistry. PMID:29133452
FledFold: A Novel Software for RNA Secondary Structure Prediction. PMID:29123460
Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies. PMID:29118447
Base pair probability estimates improve the prediction accuracy of RNA non-canonical base pairs. PMID:29107980
Tractable RNA-ligand interaction kinetics. PMID:29072147
TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs. PMID:29036420
Predicting RNA Structure with Vfold. PMID:28986779
Efficient approximations of RNA kinetics landscape using non-redundant sampling. PMID:28882001
Design of Artificial Riboswitches as Biosensors. PMID:28867802
Physics-based all-atom modeling of RNA energetics and structure. PMID:28815951
RNA folding kinetics using Monte Carlo and Gillespie algorithms. PMID:28780735
Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data. PMID:28735622
Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. PMID:28700212
What Can Human-Guided Simulations Bring to RNA Folding? PMID:28648754
Conditioning and Robustness of RNA Boltzmann Sampling under Thermodynamic Parameter Perturbations. PMID:28629618
Advanced multi-loop algorithms for RNA secondary structure prediction reveal that the simplest model is best. PMID:28586479
IntaRNA 2.0: enhanced and customizable prediction of RNA-RNA interactions. PMID:28472523
Regulation of Isoflavone Biosynthesis by miRNAs in Two Contrasting Soybean Genotypes at Different Seed Developmental Stages. PMID:28450878
Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations. PMID:28393861
In Vivo Characterization of an AHR-Dependent Long Noncoding RNA Required for Proper Sox9b Expression. PMID:28385905
A sensitivity analysis of RNA folding nearest neighbor parameters identifies a subset of free energy parameters with the greatest impact on RNA secondary structure prediction. PMID:28334976
Predicting siRNA efficacy based on multiple selective siRNA representations and their combination at score level. PMID:28317874
Thermodynamic stabilities of three-way junction nanomotifs in prohead RNA. PMID:28069889
On the conformational stability of the smallest RNA kissing complexes maintained through two G·C base pairs. PMID:28063925
Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data. PMID:27893832
Exact calculation of loop formation probability identifies folding motifs in RNA secondary structures. PMID:27852924
RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory. PMID:27756204
Group I Intron Internal Guide Sequence Binding Strength as a Component of Ribozyme Network Formation. PMID:27689977
A Method to Predict the Structure and Stability of RNA/RNA Complexes. PMID:27665593
Bridging the gap between in vitro and in vivo RNA folding. PMID:27658939
VfoldCPX Server: Predicting RNA-RNA Complex Structure and Stability. PMID:27657918
A structure-based kinetic model of transcription. PMID:27656764
Host miRNA degradation by Herpesvirus saimiri small nuclear RNA requires an unstructured interacting region. PMID:27335146
RNAiFold2T: Constraint Programming design of thermo-IRES switches. PMID:27307638
Rtools: a web server for various secondary structural analyses on single RNA sequences. PMID:27131356
Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces. PMID:27095200
Physics-based RNA structure prediction. PMID:26942214
Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus. PMID:26848969
Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis. PMID:26566145
RNA Thermodynamic Structural Entropy. PMID:26555444
IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance. PMID:26531896
Nascent RNA folding mitigates transcription-associated mutagenesis. PMID:26518484
Network Properties of the Ensemble of RNA Structures. PMID:26488894
Computational analysis of miRNA-target community network reveals cross talk among different metabolisms. PMID:26484271
Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. PMID:26451676
Structures and Energetics of Four Adjacent G·U Pairs That Stabilize an RNA Helix. PMID:26425937
Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species. PMID:26406615
Single-Molecule Imaging Reveals that Argonaute Reshapes the Binding Properties of Its Nucleic Acid Guides. PMID:26140592
Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures. PMID:26075601
Mirinho: An efficient and general plant and animal pre-miRNA predictor for genomic and deep sequencing data. PMID:26022464
RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules. PMID:26019176
A Method to Predict the 3D Structure of an RNA Scaffold. PMID:25967048
Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution. PMID:25940621
Structural features of a 3' splice site in influenza a. PMID:25909229
StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo. PMID:25886980
Functionally conserved architecture of hepatitis C virus RNA genomes. PMID:25775547
Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. PMID:25752599
A parallel implementation of the Wuchty algorithm with additional experimental filters to more thoroughly explore RNA conformational space. PMID:25695434
Fast, approximate kinetics of RNA folding. PMID:25684201
Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark. PMID:25618847
Efficient calculation of exact probability distributions of integer features on RNA secondary structures. PMID:25560710
On the normalization of the minimum free energy of RNAs by sequence length. PMID:25405875
Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble. PMID:25392423
Vfold: a web server for RNA structure and folding thermodynamics prediction. PMID:25215508
Complete RNA inverse folding: computational design of functional hammerhead ribozymes. PMID:25209235
In silico single strand melting curve: a new approach to identify nucleic acid polymorphisms in Totiviridae. PMID:25030031
Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. PMID:25026548
New strategies for evaluation and analysis of SELEX experiments. PMID:24779017
Energy parameters and novel algorithms for an extended nearest neighbor energy model of RNA. PMID:24586240
Computing the probability of RNA hairpin and multiloop formation. PMID:24559086
Asymptotic distribution of motifs in a stochastic context-free grammar model of RNA folding. PMID:24384698
Differences between cotranscriptional and free riboswitch folding. PMID:24275497
Accelerating calculations of RNA secondary structure partition functions using GPUs. PMID:24180434
Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. PMID:24134390
The paradox of dual roles in the RNA world: resolving the conflict between stable folding and templating ability. PMID:24078151
Ligand-induced stabilization of the aptamer terminal helix in the add adenine riboswitch. PMID:24051105
Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. PMID:23937650
Classification and assessment tools for structural motif discovery algorithms. PMID:23902564
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution. PMID:23812999
The DEAD-box protein Dbp2 functions with the RNA-binding protein Yra1 to promote mRNP assembly. PMID:23721653
Long-range architecture in a viral RNA genome. PMID:23614526
Control of myogenesis by rodent SINE-containing lncRNAs. PMID:23558772
The essential role of stacking adenines in a two-base-pair RNA kissing complex. PMID:23517345
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots. PMID:23503844
Pyrvinium pamoate changes alternative splicing of the serotonin receptor 2C by influencing its RNA structure. PMID:23393189
Evaluating the accuracy of SHAPE-directed RNA secondary structure predictions. PMID:23325843
Principles for understanding the accuracy of SHAPE-directed RNA structure modeling. PMID:23316814
A versatile cis-blocking and trans-activation strategy for ribozyme characterization. PMID:23155065
The Amber ff99 Force Field Predicts Relative Free Energy Changes for RNA Helix Formation. PMID:23112748
Integrating chemical footprinting data into RNA secondary structure prediction. PMID:23091593
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model. PMID:22923300
GTfold: enabling parallel RNA secondary structure prediction on multi-core desktops. PMID:22747589
The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PMID:22685560
MELTING, a flexible platform to predict the melting temperatures of nucleic acids. PMID:22591039
Thermodynamic characterization of the Saccharomyces cerevisiae telomerase RNA pseudoknot domain in vitro. PMID:22450759
Global or local? Predicting secondary structure and accessibility in mRNAs. PMID:22373926
ViennaRNA Package 2.0. PMID:22115189
Statistical potentials for hairpin and internal loops improve the accuracy of the predicted RNA structure. PMID:21889515
From structure prediction to genomic screens for novel non-coding RNAs. PMID:21829340
A folding algorithm for extended RNA secondary structures. PMID:21685061
corRna: a web server for predicting multiple-point deleterious mutations in structural RNAs. PMID:21596778
RNA Accessibility in cubic time. PMID:21388531
Different sequences show similar quaternary interaction stabilities in prohead viral RNA self-assembly. PMID:21349846
Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes. PMID:21229999
Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences. PMID:21193521
SHAPE-directed RNA secondary structure prediction. PMID:20554050
Enhanced product stability in the hammerhead ribozyme. PMID:20423112
http://nar.oxfordjournals.org/content/38/suppl_1/D280

Tags:

Tags
More detailed information about this field from each metasource.

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

structure prediction
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

nucleic acid structure analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

nucleic acids
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

rna
metasource: bio.tools
version: extracted_at: 2022-11-04T11:35:30.239686

structure nucleic acid structure structure prediction nucleic acid structure analysis nucleic acids rna

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