Related papers: Combinatorial analysis of interacting RNA molecule…
Ribonucleic Acid (RNA) can fold into shapes that perform functions in the cell. These foldings are governed by Watson-Crick base pairing, namely Adenine to Uracil and Cytosine to Guanine (A-U and G-C). The properties of the H-P…
Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE)…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
We present TT2NE, a new algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. TT2NE guarantees to find the minimum free energy…
Geometric and electronic properties of folded graphene nanoribbons (FGNRs) are investigated by first-principles calculations. These properties are mainly dominated by the competition or cooperation among stacking, curvature and edge…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…
RNA co-transcriptional folding has long been suspected to play an active role in helping proper native folding of ribozymes and structured regulatory motifs in mRNA untranslated regions. Yet, the underlying mechanisms and coding…
The study of molecule-target interaction is quite important for drug discovery in terms of target identification, hit identification, pathway study, drug-drug interaction, etc. Most existing methodologies utilize either biomedical network…
We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the…
Use of an optimization algorithm to improve performance of antennas and electromagnetic structures usually ends up in planar unusual shapes. Using rectangular conducting elements the proposed structures sometimes have connections with only…
Besides direct molecular interactions, proteins and nanoparticles embedded in or adsorbed to membranes experience indirect interactions that are mediated by the membranes. These membrane-mediated interactions arise from the membrane…
Recent advancements in machine learning techniques for protein folding motivate better results in its inverse problem -- protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to…
MicroRNAs (miRNAs) are small RNA molecules, about 22 nucleotide long, which post-transcriptionally regulate their target messenger RNAs (mRNAs). They accomplish key roles in gene regulatory networks, ranging from signaling pathways to…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…
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…
Using the atomic force microscope based break junction approach, applicable to metal point contacts and single molecule junctions, measurements can be repeated thousands of times resulting in rich data sets characterizing the properties of…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The atomic structure, stacking sequences and electronic structure of folded graphene nanoribbons (FGNRs) are investigated by first-principles calculations. It reveals that the common configurations of all FGNRs are racket-like structures…