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WebFR3D––a server for finding, aligning and analyzing recurrent RNA 3D motifs
- Nucleic Acids Res
, 2011
"... WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs ..."
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WebFR3D—a server for finding, aligning and analyzing recurrent RNA 3D motifs
CL: FASTR3D: a fast and accurate search tool for similar RNA 3D structures
- Nucleic Acids Res
"... FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an ..."
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FASTR3D is a web-based search tool that allows the user to fast and accurately search the PDB database for structurally similar RNAs. Currently, it allows the user to input three types of queries: (i) a PDB code of an RNA tertiary structure (default), optionally with specified residue range, (ii) an RNA secondary structure, optionally with primary sequence, in the dot-bracket notation and (iii) an RNA primary sequence in the FASTA format. In addition, the user can run FASTR3D with specifying additional filtering options: (i) the released date of RNA structures in the PDB database, and (ii) the experimental methods used to determine RNA structures and their least resolutions. In the output page, FASTR3D will show the user-queried RNA molecule, as well as user-specified options, followed by a detailed list of identified structurally similar RNAs. Particularly, when queried with RNA tertiary structures, FASTR3D provides a graphical display to show the structural superposition of the query structure and each of identified structures. FASTR3D is now available online at
SARA: a server for function annotation of RNA structures
- Nucleic Acids Res
, 2009
"... Recent interest in non-coding RNA transcripts has resulted in a rapid increase of deposited RNA structures in the Protein Data Bank. However, a characterization and functional classification of the RNA structure and function space have only been partially addressed. Here, we introduce the SARA progr ..."
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Recent interest in non-coding RNA transcripts has resulted in a rapid increase of deposited RNA structures in the Protein Data Bank. However, a characterization and functional classification of the RNA structure and function space have only been partially addressed. Here, we introduce the SARA program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment. The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root-mean-square approach. The likely accuracy of the SARA alignments is assessed by three different P-values estimating the statistical significance of the sequence, secondary structure and tertiary structure identity scores, respectively. Our benchmarks, which relied on a set of 419 RNA structures with known SCOR structural class, indicate that at a negative logarithm of mean P-value higher or equal than 2.5, SARA can assign the correct or a similar SCOR class to 81.4 % and 95.3 % of the benchmark set, respectively. The SARA server is freely accessible via the World Wide Web at
iPARTS: an improved tool of pairwise alignment of RNA tertiary structures
, 2010
"... iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nu-cleotides on a 2D axis using their two pseudo-torsion angles g and h. Next, we apply the affinity ..."
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iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach. In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nu-cleotides on a 2D axis using their two pseudo-torsion angles g and h. Next, we apply the affinity propagation clustering algorithm to this g-h plot to obtain an SA of 23-nt conformations. We finally use this SA to transform RNA 3D structures into 1D sequences of SA letters and continue to utilize classical sequence alignment methods to compare these 1D SA-encoded sequences and determine their structural similarities. iPARTS takes as input two RNA 3D structures in the PDB format and outputs their global alignment (for determining overall structural similarity), semiglobal alignments (for detecting structural motifs or substructures), local alignments (for finding locally similar substruc-tures) and normalized local structural alignments (for identifying more similar local substructures without non-similar internal fragments), with graph-ical display that allows the user to visually view, rotate and enlarge the superposition of aligned RNA 3D structures. iPARTS is now available online at
All-atom knowledge-based potential for RNA structure prediction and assessment
- Bioinformatics
, 2011
"... Motivation. Over the recent years, the vision that RNA simply serves as information transfer molecules has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total num-ber of experimentally solved RNA struc ..."
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Cited by 5 (2 self)
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Motivation. Over the recent years, the vision that RNA simply serves as information transfer molecules has dramatically changed. The study of the sequence/structure/function relationships in RNA is becoming more important. As a direct consequence, the total num-ber of experimentally solved RNA structures has dramatically in-creased and new computer tools for predicting RNA structure from sequence are rapidly emerging. Therefore, new and accurate meth-ods for assessing the accuracy of RNA structure models are clearly needed. Results. Here we introduce an all-atom knowledge-based potential for the assessment of RNA three-dimensional (3D) structures. We have benchmarked our new potential, called RASP, with two differ-ent decoy datasets composed of near-native RNA structures. In one of the benchmark sets, RASP was able to rank the closest model to
A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms
- 11TH WORKSHOP ON ALGORITHMS IN BIOINFORMATICS (WABI'11)
, 2011
"... We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming (Energy minimization, partition function, base-pair probabilities...) are reformula ..."
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We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming (Energy minimization, partition function, base-pair probabilities...) are reformulated within this framework, giving rise to very simple algorithms. This reformulation allows one to conceptually detach the conformation space/energy model – captured by the hypergraph model – from the specific application, assuming unambiguity of the decomposition. To ensure the latter property, we propose a new combinatorial methodology based on generating functions. We extend the set of generic applications by proposing an exact algorithm for extracting generalized moments in weighted distribution, generalizing a prior contribution by Miklos and al. Finally, we illustrate our full-fledged programme on three exemplary conformation spaces (secondary structures, Akutsu’s simple type pseudoknots and kissing hairpins). This readily gives sets of algorithms that are either novel or have complexity comparable to classic implementations for minimization and Boltzmann ensemble applications of dynamic programming.
SETTER: web server for RNA structure comparison
- Nucleic Acids Res
, 2012
"... The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple infor-mation transfer molecule. Understanding the archi-tecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is ..."
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The recent discoveries of regulatory non-coding RNAs changed our view of RNA as a simple infor-mation transfer molecule. Understanding the archi-tecture and function of active RNA molecules requires methods for comparing and analyzing their 3D structures. While structural alignment of short RNAs is achievable in a reasonable amount of time, large structures represent much bigger challenge. Here, we present the SETTER web server for the RNA structure pairwise comparison utilizing the SETTER (SEcondary sTructure-based TERtiary Structure Similarity Algorithm) algorithm. The SETTER method divides an RNA structure into the set of non-overlapping structural elements called generalized secondary structure units (GSSUs). The SETTER algorithm scales as O(n2) with the size of a GSSUs and as O(n) with the number of GSSUs in the structure. This scaling gives SETTER its high speed as the average size of the GSSU remains constant irrespective of the size of the structure. However, the favorable speed of the algorithm does not compromise its accuracy. The SETTER web server together with the stand-alone implementation of the SETTER algo-rithm are freely accessible at
RASS: a web server for RNA alignment in the joint sequence-structure space
, 2014
"... Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relation-ships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) i ..."
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Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relation-ships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) in-formation. Sequences and 3D structures contain non-overlapping sets of information that both deter-mine RNA functions. When comparing RNA 3D struc-tures, both types of information need to be taken into account. However, few methods compare RNA struc-tures using both sequence and 3D structure infor-mation. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quanti-fied by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to re-search community. The web server is located at
RNA CoSSMos: Characterization of Secondary Structure Motifs–a searchable database of secondary structure motifs in RNA three-dimensional structures
- Nucleic Acids Res
, 2012
"... three-dimensional structures ..."
