RNA contributions to the form and function of biomolecular condensates
C Roden, AS Gladfelter - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Biomolecular condensation partitions cellular contents and has important roles in stress
responses, maintaining homeostasis, development and disease. Many nuclear and …
responses, maintaining homeostasis, development and disease. Many nuclear and …
Prediction of RNA secondary structure by free energy minimization
DH Mathews, DH Turner - Current opinion in structural biology, 2006 - Elsevier
RNA secondary structure is often predicted from sequence by free energy minimization.
Over the past two years, advances have been made in the estimation of folding free energy …
Over the past two years, advances have been made in the estimation of folding free energy …
Comprehensive in vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms
Summary Severe-acute-respiratory-syndrome-related coronavirus 2 (SARS-CoV-2) is the
positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome …
positive-sense RNA virus that causes coronavirus disease 2019 (COVID-19). The genome …
ViennaRNA Package 2.0
R Lorenz, SH Bernhart… - Algorithms for molecular …, 2011 - Springer
Background Secondary structure forms an important intermediate level of description of
nucleic acids that encapsulates the dominating part of the folding energy, is often well …
nucleic acids that encapsulates the dominating part of the folding energy, is often well …
The vienna RNA websuite
Abstract The Vienna RNA Websuite is a comprehensive collection of tools for folding, design
and analysis of RNA sequences. It provides a web interface to the most commonly used …
and analysis of RNA sequences. It provides a web interface to the most commonly used …
In vivo reconstitution finds multivalent RNA–RNA interactions as drivers of mesh-like condensates
Liquid-like condensates have been thought to be sphere-like. Recently, various
condensates with filamentous morphology have been observed in cells. One such …
condensates with filamentous morphology have been observed in cells. One such …
RNAstructure: software for RNA secondary structure prediction and analysis
JS Reuter, DH Mathews - BMC bioinformatics, 2010 - Springer
Background To understand an RNA sequence's mechanism of action, the structure must be
known. Furthermore, target RNA structure is an important consideration in the design of …
known. Furthermore, target RNA structure is an important consideration in the design of …
A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed
Dynamic programming algorithms within the NUPACK software suite enable analysis of
nucleic acid sequences over complex and test tube ensembles containing arbitrary numbers …
nucleic acid sequences over complex and test tube ensembles containing arbitrary numbers …
Disease-associated mutations that alter the RNA structural ensemble
M Halvorsen, JS Martin, S Broadaway… - PLoS genetics, 2010 - journals.plos.org
Genome-wide association studies (GWAS) often identify disease-associated mutations in
intergenic and non-coding regions of the genome. Given the high percentage of the human …
intergenic and non-coding regions of the genome. Given the high percentage of the human …
The Nucleic Acid Database: new features and capabilities
B Coimbatore Narayanan, J Westbrook… - Nucleic acids …, 2014 - academic.oup.com
Abstract The Nucleic Acid Database (NDB)(http://ndbserver. rutgers. edu) is a web portal
providing access to information about 3D nucleic acid structures and their complexes. In …
providing access to information about 3D nucleic acid structures and their complexes. In …