Related papers: RNA-RNA interaction prediction based on multiple s…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
The function of a protein is defined by its interaction partners. Thus, topology-driven network alignment of the protein-protein interaction (PPI) networks of two species should uncover similar interaction patterns and allow identification…
Given the importance of non-coding RNAs to cellular regulatory functions and rapid growth of RNA transcripts, computational prediction of RNA tertiary structure remains highly demanded yet significantly challenging. Even for a short RNA…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…
Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon…
Summary: We introduce RBPBind, a web-based tool for the quantitative prediction of RNA-protein interactions. Given a user-specified RNA and a protein selected from a set of several common RNA-binding proteins, RBPBind computes the binding…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
A central problem in computational biophysics is protein structure prediction, i.e., finding the optimal folding of a given amino acid sequence. This problem has been studied in a classical abstract model, the HP model, where the protein is…