Related papers: RNA-RNA interaction prediction: partition function…
Despite the recognized importance of the multi-scale spatio-temporal organization of proteins, most computational tools can only access a limited spectrum of time and spatial scales, thereby ignoring the effects on protein behavior of the…
RNA/protein interactions play crucial roles in controlling gene expression. They are becoming important targets for pharmaceutical applications. Due to RNA flexibility and to the strength of electrostatic interactions, standard docking…
Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree…
Isoforms are mRNAs produced from the same gene site in the phenomenon called Alternative Splicing. Studies have shown that more than 95% of human multi-exon genes have undergone alternative splicing. Although there are few changes in mRNA…
The process of alpha disintegration has been studied theoretically in the framework of a microscopic superasymmetric fission model (MSAFM). The nuclear interaction potential required for the alpha decay process has been calculated by…
Motivated by the recent progress in developing high-precision relativistic chiral nucleon-nucleon interactions, we study the antinucleon-nucleon interaction in a hybrid approach where the real part of the potential is constructed in the…
RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…
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…
Non-coding RNA are functional molecules that are not translated into proteins. Their function comes as important regulators of biological function. Because they are not translated, they need not be as stable as other types of RNA. The TKF91…
Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov…
We consider a system of stochastic interacting particles with general diffusion coefficient and drift functions and we study the types of collisions that arise in them. In particular, interactions between particles are inversely…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
Many non-coding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is however a challenging task. On the other hand, thanks to the low cost of sequencing…
We derive nonstrange baryon-baryon scattering amplitudes in the nonrelativistic quark model using the ``quark Born diagram" formalism. This approach describes the scattering as a single interaction, here the one-gluon-exchange (OGE)…
Link prediction is one of the fundamental problems in network analysis. In many applications, notably in genetics, a partially observed network may not contain any negative examples of absent edges, which creates a difficulty for many…
We analyse the impact of the statistical uncertainties of the the nucleon-nucleon interaction, based on the Granada-2013 np-pp database, on the binding energies of the triton and the alpha particle using a bootstrap method, by solving the…
In this paper, we tackle a critical issue in nonparametric inference for systems of interacting particles on Riemannian manifolds: the identifiability of the interaction functions. Specifically, we define the function spaces on which the…
We predict the nature (attractive or repulsive) and range (exponentially screened or long-range power law) of the electrostatic interactions of oppositely charged and planar plates as a function of the salt concentration and surface charge…
We express the partition function for an equilibrium system of interacting particles in the canonical ensemble as a functional integration over the particles' density field. We outline a method to evaluate the partition function by…