Related papers: Eterna is Solved
In equilibrium self-assembly, microscopic building blocks spontaneously self-organize into stable structures as dictated by their interaction potentials, which limits the accessible structural features to those that correspond to global…
Structural DNA nanotechnology has advanced to the extent that extremely complex structures can be designed. Much of this advancement has been due to the development of automated DNA design and simulation tools. Typically, the tools (e.g.…
To enable emerging applications such as deep machine learning and graph processing, 3D network-on-chip (NoC) enabled heterogeneous manycore platforms that can integrate many processing elements (PEs) are needed. However, designing such…
The relationship between RNA structure and function has recently attracted interest within the deep learning community, a trend expected to intensify as nucleic acid structure models advance. Despite this momentum, the lack of standardized,…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
Proteins are macromolecules that perform essential functions in all living organisms. Designing novel proteins with specific structures and desired functions has been a long-standing challenge in the field of bioengineering. Existing…
Nested Rollout Policy Adaptation (NRPA) is a Monte Carlo search algorithm for single player games. In this paper we propose to modify NRPA in order to improve the stability of the algorithm. Experiments show it improves the algorithm for…
Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose…
RNA folding prediction remains challenging, but can be also studied using a topological mathematical approach. In the present paper, the mathematical method to compute the topological classification of RNA structures and based on matrix…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
The inverse design of RNA three-dimensional (3D) structures is crucial for engineering functional RNAs in synthetic biology and therapeutics. While recent deep learning approaches have advanced this field, they are typically optimized and…
RNA co-transcriptionality is the process where RNA sequences are spliced while being transcribed from DNA templates. This process holds potential as a key tool for molecular programming. Co-transcriptional folding has been shown to be…
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…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
Background: Designing amino acid sequences that are stable in a given target structure amounts to maximizing a conditional probability. A straightforward approach to accomplish this is a nested Monte Carlo where the conformation space is…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
In this paper we consider the problem of RNA folding with pseudoknots. We use a graphical representation in which the secondary structures are described by planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze the…
Context: Entity resolution (ER) plays a pivotal role in data management by determining whether multiple records correspond to the same real-world entity. Because of its critical importance across domains such as healthcare, finance, 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…