An increasing number of structural biology and genomics studies associate protein–DNA binding with the recognition of the three-dimensional DNA structure, or ‘DNA shape’ (Rohs et al., 2009). Source text: Zhou et al., 2013.

3DNA
Desktop

3DNA

A comprehensive software package for the analysis, reconstruction and…

A comprehensive software package for the analysis, reconstruction and visualization of three-dimensional nucleic acid structures. 3DNA can be applied to parallel and antiparallel double helices,…

DNAshapeR
Desktop

DNAshapeR

Predicts DNA shape features in an ultra-fast, high-throughput manner from…

Predicts DNA shape features in an ultra-fast, high-throughput manner from genomic sequencing data. The package takes either nucleotide sequence or genomic coordinates as input and generates various…

DNAshape
Web

DNAshape

A method and web server for predicting DNA structural features in a…

A method and web server for predicting DNA structural features in a high-throughput (HT) manner for massive sequence data. DNAshape provides the framework for the integration of DNA sequence and…

do_x3dna
Desktop

do_x3dna

Analyzes the structural fluctuations of DNA or RNA during molecular dynamics…

Analyzes the structural fluctuations of DNA or RNA during molecular dynamics simulations. do_x3dna extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to…

MINT
Desktop
Web

MINT Motif Identifier for Nucleic acids Trajectory

An automatic tool for analyzing three-dimensional structures of RNA and DNA,…

An automatic tool for analyzing three-dimensional structures of RNA and DNA, and their full-atom molecular dynamics trajectories or other conformation sets (e.g. X-ray or nuclear magnetic…

MultiRNAFold
Desktop

MultiRNAFold

Contains software for secondary structure prediction of one, two, or many…

Contains software for secondary structure prediction of one, two, or many interacting RNA or DNA molecules. MultiRNAFold is composed of three pieces of software: SimFold, PairFold and MultiFold.…

QuadBase
Web

QuadBase

Allows multiplexed putative G4 (PG4) motif mining in large number of nucleotide…

Allows multiplexed putative G4 (PG4) motif mining in large number of nucleotide sequences and also enables profiling complete prokaryotic genomes. QuadBase is linked with Ensembl's genomic…

wwPDB
Data

wwPDB Worldwide PDB

The international collaboration that manages the deposition, processing and…

The international collaboration that manages the deposition, processing and distribution of the PDB archive. The online PDB archive is a repository for the coordinates and related information for…

SIST
Desktop

SIST

A software package that analyzes sequence-dependent structural transitions in…

A software package that analyzes sequence-dependent structural transitions in kilobase length superhelical DNA molecules. The numerical algorithms in SIST are based on a statistical mechanical model…

cgDNA
Desktop

cgDNA

A package for the prediction of sequence-dependent configuration-space free…

A package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases.

A A A
UNAFold
Web

UNAFold Unified Nucleic Acid Folding

An integrated collection of programs that simulate folding, hybridization, and…

An integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. Folding (secondary structure) prediction for…

w3DNA
Web

w3DNA Web 3DNA

A user-friendly web-based interface to the 3DNA suite of programs for the…

A user-friendly web-based interface to the 3DNA suite of programs for the analysis, reconstruction, and visualization of three-dimensional (3D) nucleic-acid-containing structures, including their…

nuScore
Web

nuScore

A web-interface for estimation of the affinity of the histone core to DNA and…

A web-interface for estimation of the affinity of the histone core to DNA and prediction of nucleosome arrangement on a given sequence.

RECON
Web

RECON

Designed for constructing profiles of nucleosome potential, characterizing the…

Designed for constructing profiles of nucleosome potential, characterizing the probability of nucleosome formation along DNA sequences.

DiProDB
Data

DiProDB

A database of conformational and thermodynamic dinucleotide properties. The…

A database of conformational and thermodynamic dinucleotide properties. The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide…

DNAlive
Web

DNAlive

A tool for the analysis and graphical display of structural and physical…

A tool for the analysis and graphical display of structural and physical characteristics of genomic DNA.

DSHIFT
Web

DSHIFT

A web server for predicting chemical shifts of DNA sequences in random coil…

A web server for predicting chemical shifts of DNA sequences in random coil form or double helical B-form.

Greglist
Data

Greglist

A database listing potential G-quadruplex regulated genes.

A database listing potential G-quadruplex regulated genes.

Kinefold
Web

Kinefold

Provides a web interface for stochastic folding simulations of nucleic acids on…

Provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales.

NXSensor
Web

NXSensor

Finds nucleosome exclusion sequences, evaluates their length and spacing, and…

Finds nucleosome exclusion sequences, evaluates their length and spacing, and computes an 'accessibility score' giving the proportion of base pairs likely to be nucleosome-free.

3D-DART
Desktop
Web

3D-DART 3DNA-Driven DNA Analysis and Rebuilding Tool

Provides a convenient means of generating custom 3D structural models of DNA…

Provides a convenient means of generating custom 3D structural models of DNA with control over the local and global conformation.

Curves+
Desktop

Curves+

A nucleic acid conformational analysis program which is applicable to a wide…

A nucleic acid conformational analysis program which is applicable to a wide range of nucleic acid structures, including those with up to four strands and with either canonical or modified bases and…

DNALandscapes
Data

DNALandscapes

A database for exploring the conformational features of DNA.

A database for exploring the conformational features of DNA.

NDB
Data

NDB Nucleic Acid Database

A web portal providing access to information about 3D nucleic acid structures…

A web portal providing access to information about 3D nucleic acid structures and their complexes.

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