Related papers: Parametric analysis of RNA folding
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Adapting pre-trained foundation models for various downstream tasks has been prevalent in artificial intelligence. Due to the vast number of tasks and high costs, adjusting all parameters becomes unfeasible. To mitigate this, several…
Consider the network of all secondary structures of a given RNA sequence, where nodes are connected when the corresponding structures have base pair distance one. The expected degree of the network is the average number of neighbors, where…
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…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
Profiling is a process that finds similarities between different RNA secondary structures by extracting signals from the Boltzmann sampling. The reproducibility of profiling can be identified by the standard deviation of number of features…
The study of slope parameter is presented for elastic proton-proton and antiproton-proton scattering with taking into account the resent experimental data at high energies. The expanded logarithmic approximations allow the description of…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
Recently in \cite{34}, the role of electromagnetic field on the cracking of spherical polytropes has been investigated without perturbing charge parameter explicitly. In this study, we have examined the occurrence of cracking of anisotropic…
In this work we show that there is a direct relationship between a graph's topology and the free energy of a spin system on the graph. We develop a method of separating topological and enthalpic contributions to the free energy, and find…
Self-assembling novel ordered structures with nanoparticles has recently received much attention. Here we use computer simulations to study a two-dimensional model system characterized by a simple isotropic interaction that could be…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
Monte Carlo simulations have been used to study a vortex-free XY ferromagnet with a random field or a random anisotropy on simple cubic lattices. In the random field case, which can be related to a charge-density wave pinned by random point…
Force fields for molecular dynamics are usually developed manually, limiting their transferability and making systematic exploration of functional forms challenging. We developed a graph neural network that assigns all force field…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a…