Related papers: Ab initio RNA folding
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…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…
Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with…
RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this…
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Due to the limitation of the previous database, especially…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
The prediction of protein secondary and tertiary structures from the primary amino acid sequence is both an incredibly important and incredibly difficult problem. Accurate prediction of a protein's native structure can provide critical…
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
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,…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The RNA Inverse Folding problem comes from computational biology. The goal is to find a molecule that has a given folding. It is important for scientific fields such as bioengineering, pharmaceutical research, biochemistry, synthetic…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…