Shape detection software tools | DNA structure data analysis
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.
Allows users to simulate nucleic acid folding and hybridization for single-stranded sequences. UNAFold is a program that aims to determine folding for single-stranded RNA or DNA through combination of stochastic sampling, partition function calculations and free energy minimization. To realize melting simulations, it calculates the integrality of melting profile and not only temperatures. Images concerning hybridizations or secondary structure can be compute thanks to common formats.
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 datasets that allows virtually any organism's latest gene models or genomic assembly to be mined for the presence of PG4 motifs. The database also allows access to search in orthologues of eukaryotic genes through Ensembl's Compara. This web server provides intuitive graphical and sequence level representations of mined PG4 motifs and the results can be accessed later or be saved in convenient formats. The web server is designed, keeping in mind the requirements of both, the experimental and computational biologists, who want deep insights in to PG4 motif occurrences in their gene sets or genome of interest.
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 calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visualize statistical analyses of complex data obtained from the trajectories.
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, single-stranded forms, multi-stranded helices and complex tertiary folding motifs found in both DNA and RNA structures. The rebuilding module of 3DNA can be used to generate sequence-dependent atomic structures of nucleic acids, with or without the sugar–phosphate backbone. These structures provide a useful starting point for molecular mechanics and molecular dynamics calculations.
Provides a platform for allowing the simulation single-stranded nucleic acids melt in a solution. DINAMelt is a web application that calculates features such as ultraviolet (UV) absorbance, or concentrations of various dimer as a function of temperature. The interface allows users to set the temperature range, the nucleic acid type; the initial concentration as well as the salt conditions.
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 backbones.
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 shape analyses in genome-wide studies. The HT methodology uses a sliding-window approach to mine DNA structural information obtained from Monte Carlo simulations. It requires only nucleotide sequence as input and instantly predicts multiple structural features of DNA (minor groove width, roll, propeller twist and helix twist).
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 resonance-derived structures). For each RNA or DNA conformation MINT determines the hydrogen bonding network resolving the base pairing patterns, identifies secondary structure motifs (helices, junctions, loops, etc.) and pseudoknots. MINT also estimates the energy of stacking and phosphate anion-base interactions. For many conformations, as in a molecular dynamics trajectory, MINT provides averages of the above structural and energetic features and their evolution.
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 graphical representations for visualization and further analysis. DNAshapeR further encodes DNA sequence and shape features as user-defined combinations of k-mer and DNA shape features. The resulting feature matrices can be readily used as input of various machine learning software packages for further modeling studies.
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 that calculates the equilibrium probability of transition for each base pair in the domain. They are extensions of the original stress-induced duplex destabilization (SIDD) method, which analyzes stress-driven DNA strand separation. SIST also includes algorithms to analyze B-Z transitions and cruciform extrusion. The SIST pipeline has an option to use the DZCBtrans algorithm, which analyzes the competition among these three transitions within a superhelical domain.
Allows conformational analysis of Martini-based coarse-grained double strand DNA molecules. cgHeliParm enables the direct analysis of coarse-grained DNA trajectories avoiding an additional transformation to atomistic trajectories. The software (1) reads CG Martini GROMACS input files using the MDAnalysis package, (2) calculates physical descriptors, and (3) generates output files without conversion into atomistic resolution. The package includes R scripts for calculating general statistical values and creating the corresponding histograms.
Provides coarse-grained and multi-scaled models. YUP is a molecular modeling program concentrated on molecular simulations (mechanics) and on reduced representation and multiscale modeling. This method is based on Yammp, a molecular mechanics package with the specific purpose of facilitating coarse-grained modeling. It can be used for all-atom modeling, and its principal applications have been aimed at tackling very large systems with reduced representations.
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. SimFold predicts the minimum free energy (MFE) secondary structure of a given input RNA or DNA sequence. PairFold predicts the MFE secondary structure of two interacting RNA or DNA molecules, and suboptimal structures. MultiFold predicts the MFE secondary structure of three or more RNA/DNA input sequences.
Allows users to build three-dimensional structures. 3D-NuS builds 3D models of right handed intra/intermolecular DNA/RNA duplexes and RNA-DNA hybrid duplexes, left handed Z-DNA/Z-RNA duplexes, triplexes and intra/intermolecular G-quadruplexes. The software can also generate a range of conformations for a given sequence. It can be useful to explore dynamics of aforementioned molecules in docking and simulation studies and to understand the structural characteristics of nucleic acids under normal and diseased conditions. Models can be downloaded in PDB format or visualized on the webpage.
Combines theoretical calculations with the knowledge contained in the experimental X-ray crystal structure databases of oligonucleotides to predict the conformational properties of DNA oligomers. PREDICTOR is a method available via a web interface.
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