Results 1 - 10
of
35
DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities
, 2007
"... ..."
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 ..."
Abstract
-
Cited by 18 (5 self)
- Add to MetaCart
(Show Context)
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 ..."
Abstract
-
Cited by 12 (1 self)
- Add to MetaCart
(Show Context)
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 ..."
Abstract
-
Cited by 12 (1 self)
- Add to MetaCart
(Show Context)
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 ..."
Abstract
-
Cited by 9 (0 self)
- Add to MetaCart
(Show Context)
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 ..."
Abstract
-
Cited by 5 (2 self)
- Add to MetaCart
(Show Context)
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
Biological insights from topology independent
, 2011
"... doi:10.1093/nar/gkr348 ..."
(Show Context)
183 SUFFIX TECHNIQUES AS A RAPID METHOD FOR RNA SUBSTRUCTURE SEARCH
"... The RNA Ontology Consortium recently proposed a two-letter representation of the RNA backbone conformation. In this study, we compare the suite notation to a custom string representation that utilizes η – θ pseudotorsion angles. Both representations were used to assess similarity and self-similarity ..."
Abstract
-
Cited by 1 (1 self)
- Add to MetaCart
(Show Context)
The RNA Ontology Consortium recently proposed a two-letter representation of the RNA backbone conformation. In this study, we compare the suite notation to a custom string representation that utilizes η – θ pseudotorsion angles. Both representations were used to assess similarity and self-similarity in several RNA structure datasets. For the detection of similarities between two RNA structures we are utilizing suffix techniques that allow for the detection of substructure similarity within some degree of inexactness. The suite representation as well as the pseudotorsion representation was tested on four diverse RNA datasets. The possibility to detect structural similarities on these datasets allowed to recover many homologous structural elements that have implications for further understanding of the RNA apparatus in Systems Biology. The software as well as the utilized datasets are freely available from
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 ..."
Abstract
-
Cited by 1 (0 self)
- Add to MetaCart
(Show Context)
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 ..."
