scholarly journals Linking RNA Secondary Structure to the Free Energy of Tertiary Structure Folding through Coarse-Grained Models

2014 ◽  
Vol 106 (2) ◽  
pp. 284a
Author(s):  
Anthony M. Mustoe ◽  
Hashim M. Al-Hashimi ◽  
Charles L. Brooks
Keyword(s):  
Free Energy ◽  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Tertiary Structure ◽  
Coarse Grained

scholarly journals 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 287 ◽  
Author(s):  
Bernhard C. Thiel ◽  
Irene K. Beckmann ◽  
Peter Kerpedjiev ◽  
Ivo L. Hofacker
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Tertiary Structure ◽  
3D Structure ◽  
Coarse Grained ◽  
Helix Axis ◽  
Structure Representation ◽  
File Formats ◽  
3D Information ◽  
Stacking Patterns

We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudoknots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.

scholarly journals 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 287
Author(s):  
Bernhard C. Thiel ◽  
Irene K. Beckmann ◽  
Peter Kerpedjiev ◽  
Ivo L. Hofacker
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Tertiary Structure ◽  
3D Structure ◽  
Coarse Grained ◽  
Helix Axis ◽  
Structure Representation ◽  
File Formats ◽  
3D Information ◽  
Stacking Patterns

We present forgi, a Python library to analyze the tertiary structure of RNA secondary structure elements. Our representation of an RNA molecule is centered on secondary structure elements (stems, bulges and loops). By fitting a cylinder to the helix axis, these elements are carried over into a coarse-grained 3D structure representation. Integration with Biopython allows for handling of all-atom 3D information. forgi can deal with a variety of file formats including dotbracket strings, PDB and MMCIF files. We can handle modified residues, missing residues, cofold and multifold structures as well as nucleotide numbers starting at arbitrary positions. We apply this library to the study of stacking helices in junctions and pseudo knots and investigate how far stacking helices in solved experimental structures can divert from coaxial geometries.

scholarly journals The Globular State of the Single-Stranded RNA: Effect of the Secondary Structure Rearrangements

2015 ◽  
Vol 2015 ◽  
pp. 1-6
Author(s):  
Zareh A. Grigoryan ◽  
Armen T. Karapetian
Keyword(s):  
Phase Transition ◽  
Secondary Structure ◽  
Characteristic Time ◽  
Tertiary Structure ◽  
Mutual Influence ◽  
Coarse Grained ◽  
Nonequilibrium Phase Transition ◽  
Nonequilibrium Phase ◽  
Coarse Grained Model ◽  
Structure Rearrangement

The mutual influence of the slow rearrangements of secondary structure and fast collapse of the long single-stranded RNA (ssRNA) in approximation of coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary structure rearrangement is much longer than that for the formation of the tertiary structure. A nonequilibrium phase transition of the 2nd order has been observed.

scholarly journals RAG-Web: RNA structure prediction/design using RNA-As-Graphs

2019 ◽  
Author(s):  
Grace Meng ◽  
Marva Tariq ◽  
Swati Jain ◽  
Shereef Elmetwaly ◽  
Tamar Schlick
Keyword(s):  
Secondary Structure ◽  
Rna Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Tree Graph ◽  
Rna Structure Prediction ◽  
Tree Graphs

Abstract Summary We launch a webserver for RNA structure prediction and design corresponding to tools developed using our RNA-As-Graphs (RAG) approach. RAG uses coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph theory to analyze and advance RNA structure discovery. Our webserver consists of three modules: (a) RAG Sampler: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary topologies, (b) RAG Builder: builds three-dimensional atomic models from candidate graphs generated by RAG Sampler, and (c) RAG Designer: designs sequences that fold onto novel RNA motifs (described by tree graph topologies). Results analyses are performed for further assessment/selection. The Results page provides links to download results and indicates possible errors encountered. RAG-Web offers a user-friendly interface to utilize our RAG software suite to predict and design RNA structures and sequences. Availability and implementation The webserver is freely available online at: http://www.biomath.nyu.edu/ragtop/. Supplementary information Supplementary data are available at Bioinformatics online.

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