Related papers: Pattern Matching and Local Alignment for RNA Struc…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
We show the expected order of RNA saturated secondary structures of size $n$ is $\log_4n(1+O(\frac{\log_2n}{n}))$, if we select the saturated secondary structure uniformly at random. Furthermore, the order of saturated secondary structures…
Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
We study plane trees as a model for RNA secondary structure, assigning energy to each tree based on the Nearest Neighbor Thermodynamic Model, and defining a corresponding Gibbs distribution on the trees. Through a bijection between plane…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…
Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small alpha protein domains have hidden…
Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…
Most of the current understanding of structure-property relations at the molecular and the supramolecular scales can be formulated in terms of the stability of and the interactions between a limited number of recurring structural motifs…
This letter reports complete sets of two-fold symmetries between partitions of the universal genetic code. By substituting bases at each position of the codons according to a fixed rule, it happens that properties of the degeneracy pattern…
Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the…
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all sequences of fixed length certain shapes are…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
A hierarchical model for the growth of planar arch structures for RNA secondary structures is presented, and shown to be equivalent to a tree-growth model. Both models can be solved analytically, giving access to scaling functions for large…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…