Related papers: AligNet: Alignment of Protein-Protein Interaction …

Physics-Informed Neural Networks (PINNs) have become a prominent application of deep learning in scientific computation, as they are powerful approximators of solutions to nonlinear partial differential equations (PDEs). There have been…

Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses…

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…

Physics-Informed Neural Networks (PINNs) have emerged as a tool for approximating the solution of Partial Differential Equations (PDEs) in both forward and inverse problems. PINNs minimize a loss function which includes the PDE residual…

We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…

Regular physics-informed neural networks (PINNs) predict the solution of partial differential equations using sparse labeled data but only over a single domain. On the other hand, fully supervised learning models are first trained usually…

The sheer amounts of biological data that are generated in recent years have driven the development of network analysis tools to facilitate the interpretation and representation of these data. A fundamental challenge in this domain is the…

Motivation: Protein interactions are fundamental building blocks of biochemical reaction systems underlying cellular functions. The complexity and functionality of such systems emerge not from the protein interactions themselves but from…

Physics Informed Neural Network (PINN) is a scientific computing framework used to solve both forward and inverse problems modeled by Partial Differential Equations (PDEs). This paper introduces IDRLnet, a Python toolbox for modeling and…

A variety of methods have been proposed for structure similarity calculation, which are called structure alignment or superposition. One major shortcoming in current structure alignment algorithms is in their inherent design, which is based…

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…

The application of the Physics-Informed Neural Networks (PINNs) to forward and inverse analysis of pile-soil interaction problems is presented. The main challenge encountered in the Artificial Neural Network (ANN) modelling of pile-soil…

Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…

Protein Contact Network (PCN) is a powerful tool for analysing the structure and function of proteins. In particular, PCN has been used for disclosing the molecular features of allosteric regulation through PCN clustering. Such analysis is…

Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…

Deep learning approaches achieved significant progress in predicting protein structures. These methods are often applied to protein-protein interactions (PPIs) yet require Multiple Sequence Alignment (MSA) which is unavailable for various…

Data on molecular interactions is increasing at a tremendous pace, while the development of solid methods for analyzing this network data is lagging behind. This holds in particular for the field of comparative network analysis, where one…

The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…

With the advent of high-throughput wet lab technologies the amount of protein interaction data available publicly has increased substantially, in turn spurring a plethora of computational methods for in silico knowledge discovery from this…

In the present article, we propose a paradigm shift on evolving Artificial Neural Networks (ANNs) towards a new bio-inspired design that is grounded on the structural properties, interactions, and dynamics of protein networks (PNs): the…