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In living cells, intrinsically disordered proteins (IDPs), such as FUS and DDX4, undergo phase separation, forming biomolecular condensates. Using molecular dynamics simulations, we investigate their behavior in their respective homogenous…
Regression problems have been more and more embraced by deep learning (DL) techniques. The increasing number of papers recently published in this domain, including surveys and reviews, shows that deep regression has captured the attention…
We predict analytically that diagonal correlations of amino acid positions within protein sequences statistically enhance protein propensity for nonspecific binding. We use the term 'promiscuity' to describe such nonspecific binding.…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
In this paper, a new interval type-2 fuzzy neural network able to construct non-separable fuzzy rules with adaptive shapes is introduced. To reflect the uncertainty, the shape of fuzzy sets considered to be uncertain. Therefore, a new form…
Proteins congregate into complexes to perform fundamental cellular functions. Phenotypic outcomes, in health and disease, are often mechanistically driven by the remodeling of protein complexes by protein coding mutations or cellular…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including…
Theory of operators generated by binary fuzzy relations is highly increasing for its nature and applicability. The main goal of the paper is to present several representation theorems for operators induced by fuzzy relations (for example…
Patchy particles are considered to be a good model for protein aggregation. We calculate the equilibrium phase diagram of two-patch colloidal particles undergoing aggregation along with isotropic potential. This investigation demonstrates…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…
In this paper we establish a link between fuzzy and preferential semantics for description logics and Self-Organising Maps, which have been proposed as possible candidates to explain the psychological mechanisms underlying category…
The feature selection in a traditional binary classification algorithm is always used in the stage of dataset preprocessing, which makes the obtained features not necessarily the best ones for the classification algorithm, thus affecting…
The anisotropic feature of charge transfer reactions in realistic proteins cannot be ignored, due to the highly complex chemical structure of bio-molecules. In this work, we have performed the first large-scale quantitative assessment of…
Self-assembly in natural and synthetic molecular systems can create complex aggregates or materials whose properties and functionality rises from their internal structure and molecular arrangement. The key microscopic features that control…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…