Assists users to analyze nucleic acids structures and trajectories. Barnaba includes features for: computing various structural parameters, performing dimensionality reduction and clustering, back-calculating experimental quantities form structures and constructing elastic network models. Moreover, this tool uses the capabilities of MDTraj (a python library) for reading/writing trajectory files, and thus supports many different formats.
A graph theoretical program that can search for 3D patterns of base arrangements by representing the bases as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. The input files for NASSAM are PDB formatted 3D coordinates. This web server can be used to identify matches of base arrangement patterns in a query structure to annotated patterns that have been reported in the literature or that have possible functional and structural stabilization implications.
Simulates RNA folding and predicts 3D structure. SimRNA is based on a coarse-grained representation of RNA molecules and uses the Monte Carlo method. It can predict RNA 3D structure from sequence alone and use additional structural information in the form of secondary structure restraints, distance restraints that define the local arrangement of certain atoms. The tool can jump-start the simulation with a 3D structure provided in a PDB file.
A software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach.
Allows accurate prediction of short (<50 nucleotides) tertiary RNA structures starting from primary sequences. The new version of the iFoldRNA server permits the prediction of tertiary structure of RNAs as long as a few hundred nucleotides. This substantial increase in the server capacity is achieved by utilization of experimental information such as base-pairing and hydroxyl-radical probing.
A web server capable of predicting core structures of telomerase RNA (TR) in yeast genomes. The aim of TRFolder-W is to use the five core structures as fundamental units to predict potential TR genes for yeast, and to provide a user-friendly interface. Moreover, the application of TRFolder-W can be extended to predict the characteristic structure on species other than fungal species.
A program for annotating atomic-resolution RNA 3D structure files and searching them efficiently to locate and compare RNA 3D structural motifs. WebFR3D provides on-line access to the central features of FR3D, including geometric and symbolic search modes, without need for installing programs or downloading and maintaining 3D structure data locally. In geometric search mode, WebFR3D finds all motifs similar to a user-specified query structure. In symbolic search mode, WebFR3D finds all sets of nucleotides making user-specified interactions.
Establishes a central, redistributable workbench for scientists and programmers working with RNA-related data. The RNA workbench builds a sustainable community around it. This platform is unique in combining available tools, workflows and training material, as well as providing easy access for experimentalists. It serves as a central hub for programmers, which can easily integrate and deploy their existing or novel tools and workflows.
An integrated and automated tool for analyzing and annotating RNA tertiary structures. DSSR identifies canonical and noncanonical base pairs, including those with modified nucleotides, in any tautomeric or protonation state. It detects higher-order coplanar base associations, termed multiplets. DSSR finds arrays of stacked pairs, classifies them by base-pair identity and backbone connectivity, and distinguishes a stem of covalently connected canonical pairs from a helix of stacked pairs of arbitrary type/linkage. DSSR identifies coaxial stacking of multiple stems within a single helix and lists isolated canonical pairs that lie outside of a stem. The program characterizes ‘closed’ loops of various types (hairpin, bulge, internal, and junction loops) and pseudoknots of arbitrary complexity. Notably, DSSR employs isolated pairs and the ends of stems, whether pseudoknotted or not, to define junction loops.
A knowledge-based potential that combines distance-dependent and dihedral-dependent energies. The benchmarks on different testing datasets all show that 3dRNAscore are more efficient than existing evaluation methods in recognizing native state from a pool of near-native states of RNAs as well as in ranking near-native states of RNA models.
A computational server for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models. Our approach is based on the idea of local neighborhood, defined as a set of atoms included in the sphere centered around a user-defined atom. A unique feature of the RNAssess is the simultaneous visualization of the model-reference structure distance at different precision levels, from the individual residues to the entire molecules.
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.
Provides seamless, nucleotide-level access to high-quality, curated sequence alignments for rRNAs of all major phylogenetic domains, using residue numbers taken directly from representative, atomic-resolution 3D structures selected from PDB/NDB for completeness and quality. R3D-2-MSA is extensible to additional classes of structured RNAs. Its programmatic interface facilitates the use of RNA sequence variability data in a wide range of bioinformatic applications, including RNA 3D modeling, evolutionary studies and identification of non-coding RNA genes in genomes. The server also provides an attractive, easy-to-use interface for manual use by bench scientists and students learning about RNA structure and evolution.
A graph theoretical algorithm implemented as a web server that is able to search for unbroken networks of hydrogen-bonded base interactions and thus provide an accounting of such interactions in RNA 3D structures. COGNAC is also able to compare the hydrogen bond networks between two structures and from such annotations enable the mapping of atomic level differences that may have resulted from conformational changes due to mutations or binding events.
Uses an integer programming framework to predict RNA 2D-3D structures. RNA-MoIP is an accurate hybrid method that uses RNA secondary structure templates in which it inserts candidate RNA 3D motifs. This server was designed with the goal of making the unique IP-based approach to tertiary structure prediction available to all users. It can be used as a valuable tool for applications requiring both fast and accurate 3D structure predictions, such as RNA structure, function and interaction prediction.
Calculates a thermodynamic matcher (TDM) by using a runtime heuristic for probabilistic shape analysis. RapidShapes can compute sequences with more than 400 nucleotides. This tool processes shapes above a specified alpha-threshold by producing a list of interesting shapes. It builds some specialized folding programs for each shape to measure its share of Boltzmann probability. It also uses a pipeline structure to predict exact probabilities of RNA shapes.
Computes energy scores for assessing the stability of RNA structures. WebRASP receives as input a PDB file containing the atomic coordinates of the RNA structure and calculates the energy profile and total energy score of the molecule. The server displays the results graphically and the visualization can be modified by the user interactively.
Provides an RNA conformational morphing procedure. KGS is all-atom algorithm to compute motions of conformational change directly and exactly in the secondary structure constraint manifold between two conformers. It was implemented with secondary-structure-constraint-manifold-modulated conformational changes and clash-avoiding. This procedure first aligns the initial and the goal conformation. Next, it deforms the molecule.
A method to tackle a key step in the RNA 3D structure prediction problem, the prediction of the nucleotide interactions that constitute the desired 3D structure. The research is based on a novel graph model, called a backbone k-tree, to tightly constrain the nucleotide interaction relationships considered for RNA 3D structures.
A software tool for RNA modeling that uses an RNA-specific knowledge-based potential in a coarse-grained molecular dynamics engine to generate plausible 3D structures. We demonstrate NAST's capabilities by using only secondary structure and tertiary contact predictions to generate, cluster, and rank structures.
Aims to solve the conformational sampling problem. BARNACLE describes RNA structure in a natural, continuous space. It permits sampling 3-D conformations that are RNA-like on a short length scale. This tool is based on a dynamic Bayesian network (DBN) combined with directional statistics. It is interpretable in the language of statistical physics that makes it attractive from a theoretical viewpoint.
A program for sampling coarse grain 3D RNA structures. Ernwin uses the coarse grain representation presented in the forgi library. The simplest scenario involves providing a sequence and a secondary structure as input and obtaining coarse-grain tertiary structures as output.
Proposes an RNA fragment assembly method that preserves RNA global secondary structure while sampling conformations. RSIM provides a fully automated application predicting RNA tertiary structures from secondary structure constraints using fragment assembly. These tertiary structures are further refined with Monte Carlo simulations utilizing a sampling method, an expanded statistical potential, and a diverse fragment library. Furthermore, RSIM tracks simulation paths during refinement. This allows representation of the predicted RNA conformational space as a graph with secondary structures as nodes and simulation paths as edges. Graph theoretic analysis can then be applied to predict regions in the conformational space most likely to contain native-like RNA structures.
Provides a method for genome-scale characterization of RNA tertiary structure. RNAsnap yields a robust performance in cross-validation and independent tests. It was developed as a machine-learning model on protein-bound RNA structures for RNA solvent accessibility prediction. Genome-scale application to mRNA indicates a positive correlation to in vivo genome-scale measured RNA reactivity to dimethylsulphate (DMS).
Recognizes the secondary and tertiary structures of RNA. PRI-Modeler analyzes the hydrogen bond and van der Waals interactions between protein and RNA from the three-dimensional atomic coordinates of protein-RNA complexes in the protein data bank. It identifies base pairs and classifies base pairs into 28 types to extract secondary and tertiary structures. It can analyze multiple PDB files at once and provides the analysis report on protein-RNA interactions in all the PDB files analyzed.
A Java application for the design of RNA nanoscale structures from building blocks. Among other things, it can accomplish the following: 1) detection, extraction and annotation of RNA structural elements, 2) use of RNA building blocks for assembling larger structures, 3) combinatorial search of building blocks 4) optimization of building block positions 5) topology classification 6) sequence Optimization (i.e. sequence design for self-assembly into the given topology).
An algorithm that can compute the expected number of neighbors, or expected network degree, of an input sequence. For RNA sequences from the Rfam database, the expected degree is significantly less than the constrained minimum free energy structure, defined to have minimum free energy (MFE) over all structures consistent with the Rfam consensus structure.
Classifies a family of protein structures or macromolecular complexes according to their geometric core. Lcore is a web server that computes a geometrical core and can be applied to determine the conserved features of families of macro molecular complexes. Users can set various options including the desired distance threshold, the core identifier for chain superimposition as well as the alternative core new atoms.
Provides a user friendly tool for the prediction of RNA structure and stability. Vfold offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization.
Implements two cubic time algorithms to compute the RNA thermodynamic structural entropy H(s) of a sequence s. Structural entropy is computed from the expected free energy of the sequence <E> and the partition function Z(s). Structural entropy H(s)=<E>/RT + ln Z(s)
A software to compute a sampling of RNA 3D structure from a secondary structure. GARN is a coarse-grained method for sampling, based on game theory and knowledge-based potentials. Game theory is a suitable tool for understanding systems in which the players have preferences for certain solutions. It favors local, egotistical choices rather than searching for a global optimum. GARN is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints.
Using primary and secondary structure information of an RNA molecule, the program automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement.
Computes the dual partition function Z of all RNA nucleotide sequences a compatible with target structure s0. RNAdualPF generates sequences which have low free energy with respect to a user-specified target structure s0 – i.e. the inherent bias of RNAdualPF is known, unlike the situation of other inverse folding algorithms. RNAdualPF additionally allows the user to specify IUPAC codes to constrain certain nucleotide positions as well as to control the GC-content of all generated sequences.
Models nucleobase and nucleoside residue conformations in fixed-backbone RNA 3D structures. RNAfitme looks for the optimal mutual arrangement of nucleobase/nucleoside residues in the RNA structure. It can choose subset of promising candidates and control reconstruction accuracy from a global perspective. This tool can diminish the number of invalid contacts in the modeled structure.
Allows to explore detailed aspects of topological constraints in complex RNA systems. TOPRNA can isolate the effects of topological constraints on RNA structure. It was used to reevaluate the role of topological constraints in two-way junction bulge motifs. The tool was applied to study the pseudoknot of the preQ1 riboswitch and to study the topological constraints of the four-way junction of tRNA.
An algorithm to evaluate 3D RNA structure. PTRNAmark doesn’t only combine nucleotides’ mutual and self energies but also fully considers the specificity of every RNA. It is based on all-heavy-atom knowledge-based statistical potential. PTRNAmark can fully consider the characteristic of every RNA model and the specificity of physical interaction. It turns out that PTRNAmark performs better than 3DRNAScore, RASP, KB potentials and ROSETTA in ranking a tremendous amount of near-native RNA tertiary structures as well as recognizing native state from a pool of near-native states of RNAs.
Allows to manipulate RNA structures interactively. HiRE-RNA is a coarse-grained model for RNA structure prediction and the dynamical study of RNA folding. By mean of a molecular visualization software, UnityMol, users can pull atoms and discover how these molecules behave and how it is related to the function. Users can then submit their simulated RNA structures which evaluated and scored based on energy calculations.
Automates design of RNA molecules with complex 3D folds. RNAMake is a toolkit contains a library of hundreds of unique motifs and a path-finding algorithm to connect any two points in 3D space at a desired relative orientation using an RNA segment. These motifs are small modular fragments of RNA that are believed to fold independently, thus attaching them together with helix flanking both sides allows users of RNAMake to build large segments of RNA with a high success rate of forming the predicted structure in vitro.
Assists in looking at the 3D structures of proteins, DNA, RNA, and their complexes. FirstGlance works within a web browser and enables the readers of scientific journals to see the main features of newly published 3D models without installing anything. It works in all popular web browsers and computer platforms. It provides a user-interface to the molecular visualization program Jmol.
Assesses de novo RNA structure prediction. RNA-Puzzles aims to: (1) evaluate the cutting edge of RNA structure prediction techniques; (2) compare the different methods and tools; (3) determine what has still to be done to achieve an ultimate solution to the structure prediction problem; (4) promote the available methods and guide potential users in the choice of suitable tools for different problems.
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