Related papers: Protein folding analysis using features obtained b…
Protein structure prediction remains a challenge in the field of computational biology. Traditional protein structure prediction approaches include template-based modelling (say, homology modelling, and threading), and ab initio. A…
We present a dynamical model of lipoprotein metabolism derived by combining a cascading process in the blood stream and cellular level regulatory dynamics. We analyse the existence and stability of equilibria and show that this…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
Persistent homology is a topological feature used in a variety of applications such as generating features for data analysis and penalizing optimization problems. We develop an approach to accelerate persistent homology computations…
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were…
We study the thermodynamic and kinetic consequences of the competition between single-protein folding and protein-protein aggregation using a phenomenological model, in which the proteins can be in the unfolded (U), misfolded (M) or folded…
Using Monte Carlo dynamics and the Monte Carlo Histogram Method, the simple three-dimensional 27 monomer lattice copolymer is examined in depth. The thermodynamic properties of various sequences are examined contrasting the behavior of good…
De novo prediction of protein structures, the prediction of structures from amino-acid sequences which are not similar to those of hitherto resolved structures, has been one of the major challenges in molecular biophysics. In this paper, we…
Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action…
A novel approach to protein folding dynamics is presented. We suggest that folding of protein may be mediated via interaction with solitons which propagate along the molecular chain. A simple toy model is presented in which a Sine-Gordon…
We develop a path-based approach to continuous-time random walks on networks with arbitrarily weighted edges. We describe an efficient numerical algorithm for calculating statistical properties of the stochastic path ensemble. After…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
Figuring out small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many virtual and real drug-discovery scenarios. Since it is not always easy to find such binding sites based on…
We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
We study the thermodynamical properties of a topology-based model proposed by Galzitskaya and Finkelstein for the description of protein folding. We devise and test three different mean-field approaches for the model, that simplify the…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
In this paper we develop a novel Topological Data Analysis (TDA) approach for studying graph representations of time series of dynamical systems. Specifically, we show how persistent homology, a tool from TDA, can be used to yield a…
Spatial transcriptomics studies are becoming increasingly large and commonplace, necessitating simultaneous analysis of a large number of spatially resolved variables. Correspondingly, a diverse range of methodologies have been proposed to…